UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549
                                  SCHEDULE 13D
                   Under the Securities Exchange Act of 1934
                               (Amendment No. __)*


                                  AEROGEN, INC.
--------------------------------------------------------------------------------
                                (Name of Issuer)

                     Common Stock, par value $0.001 per share
--------------------------------------------------------------------------------
                         (Title of Class of Securities)

                                    007779309
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                                 (CUSIP Number)

   Mitchell D. Kaye, Manager                        with a copy to:
   Xmark Asset Management, LLC                      Steven E. Siesser, Esq.
   152 West 57th Street                             Lowenstein Sandler PC
   21st Floor                                       65 Livingston Avenue
   New York, New York  10019                        Roseland, New Jersey  07068
   (212) 247-8200                                   (973) 597-2506
--------------------------------------------------------------------------------
                 (Name, Address and Telephone Number of Person
                Authorized to Receive Notices and Communications)

                                November 4, 2004
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             (Date of Event which Requires Filing of this Statement)


If the filing person has previously  filed a statement on Schedule l3G to report
the  acquisition  that is the subject of this  Schedule  13D, and is filing this
schedule  because of Sections 240.13d-1(e),  240.13d-1(f) or 240.13d-1(g), check
the following box. [ ]

Note:  Schedules  filed in paper format shall include a signed original and five
copies of the schedule, including all exhibits.  See Section 240.13d-7 for other
parties to whom copies are to be sent.

* The remainder of this cover page shall be filled out for a reporting  person's
initial filing on this form with respect to the subject class of securities, and
for  any  subsequent   amendment   containing   information  which  would  alter
disclosures provided in a prior cover page.

The information required on the remainder of this cover page shall not be deemed
to be "filed" for the purpose of Section 18 of the  Securities  Exchange  Act of
1934 ("Act") or otherwise  subject to the liabilities of that section of the Act
but  shall be  subject  to all other  provisions  of the Act  (however,  see the
Notes).




Cusip No.         007779309
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1.  Names of Reporting Persons.  I.R.S. Identification Nos. of above persons
   (entities only):
                       Xmark Asset Management, LLC
                               13-3954392
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2.  Check the Appropriate Box if a Member of a Group (See Instructions):
         (a)                  Not 
         (b)               Applicable
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3.  SEC Use Only
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4.  Source of Funds (See Instructions):  WC
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5.  Check if  Disclosure  of  Legal  Proceedings Is  Required Pursuant  to Items
    2(d) or 2(e):                 Not Applicable
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6.  Citizenship or Place of Organization:  New York, United States
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    Number of                      7. Sole Voting Power:                  *
                                      ------------------------------------------
    Shares Beneficially            8. Shared Voting Power:                *
                                      ------------------------------------------
    Owned by
    Each Reporting                 9. Sole Dispositive Power:             *
                                      ------------------------------------------
    Person With                   10. Shared Dispositive Power:           *
                                      ------------------------------------------
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11. Aggregate Amount Beneficially Owned by Each Reporting Person:   1,685,596*
--------------------------------------------------------------------------------
12. Check if the Aggregate Amount in Row (11) Excludes Certain Shares
    (See Instructions):          Not Applicable
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13. Percent of Class Represented by Amount in Row (11):   26.1%*
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14. Type of Reporting Person (See Instructions):  IA
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*   Xmark Asset Management, LLC, a New York limited  liability  company ("XAM"),
serves as investment  manager for each of Xmark Fund,  L.P., a Delaware  limited
partnership  ("Xmark  LP"),  and Xmark Fund,  Ltd.,  a Cayman  Islands  exempted
company  ("Xmark Ltd").  In such  capacity,  XAM possesses the power to vote and
direct the  disposition of all securities  held by Xmark LP and Xmark Ltd. As of
November  4, 2004,  Xmark LP is the holder of (i) 74,025  shares  (the "Xmark LP
Preferred") of the Series A-1 Preferred  Stock,  par value $0.001 per share (the
"Preferred  Stock") of Aerogen,  Inc., a Delaware  corporation  (the "Company"),
which are presently  convertible  into 740,250  shares of the  Company's  common
stock, par value $0.001 per share (the "Common Stock"),  (ii) warrants  expiring
on March 22, 2009,  which  entitle  Xmark LP to purchase  up to an  aggregate of
339,600  shares of Common  Stock at an  exercise  price of $3.25 per share  (the
"Xmark LP March 2009  Warrants"),  which exercise price is subject to adjustment
as set forth in the Xmark LP March 2009 Warrants, (iii) warrants expiring on May
11,  2009,  which  entitle  Xmark LP to purchase up to an  aggregate  of 400,650
shares of Common  Stock at an  exercise  price of $3.25 per share (the "Xmark LP
May 2009  Warrants",  and together  with the Xmark LP March 2009  Warrants,  the
"Xmark LP Warrants"), which exercise price is subject to adjustment as set forth
in the Xmark LP May 2009  Warrants  and (iv) 8,411 shares of Common Stock issued
in lieu of the cash payment of quarterly  dividends on the Preferred  Stock held
by Xmark LP for the  quarters  ended  March 31,  2004 and June 30,  2004.  As of
November 4, 2004,  Xmark Ltd is the holder of (i) 92,641  shares (the "Xmark Ltd
Preferred") of Preferred  Stock,  which are presently  convertible  into 926,410
shares of Common Stock,  (ii) warrants expiring on March 22, 2009, which entitle
Xmark Ltd to purchase up to an aggregate of 425,010 shares of Common Stock at an
exercise price of $3.25 per share (the "Xmark Ltd March 2009  Warrants"),  which
exercise price is subject to adjustment as set forth in the Xmark Ltd March 2009
Warrants,  (iii) warrants  expiring on May 11, 2009,  which entitle Xmark Ltd to
purchase up to an  aggregate  of 501,400  shares of Common  Stock at an exercise





price of $3.25 per share (the "Xmark Ltd May 2009  Warrants",  and together with
the Xmark Ltd March 2009  Warrants,  the "Xmark Ltd  Warrants"),  which exercise
price is subject to  adjustment  as set forth in the Xmark Ltd May 2009 Warrants
and (iv) 10,525  shares of Common  Stock  issued in lieu of the cash  payment of
quarterly  dividends on the  Preferred  Stock held by Xmark Ltd for the quarters
ended March 31, 2004 and June 30, 2004. The terms of the Xmark LP Preferred, the
Xmark Ltd Preferred,  the Xmark LP Warrants and the Xmark Ltd Warrants  preclude
each of Xmark LP and Xmark Ltd from  converting  the Xmark LP Preferred  and the
Xmark  Ltd  Preferred  or  exercising  the Xmark LP  Warrants  and the Xmark Ltd
Warrants if the  conversion or exercise  thereof would result in Xmark LP, Xmark
Ltd  and/or  their  affiliates  beneficially  owning  in  excess of 4.99% of the
Company's  outstanding  Common Stock  following any such  conversion or exercise
(the "Issuance Limitation").  Each such Issuance Limitation is waivable by Xmark
LP and Xmark Ltd, respectively, providing 61 days' advance written notice to the
Company.  On  November 3, 2004,  Xmark LP and Xmark Ltd each  provided a written
waiver of the  Issuance  Limitation  to the Company with respect to the Xmark LP
Preferred  and the Xmark Ltd  Preferred.  As a result  of this  waiver  and as a
result of the fact that XAM  possesses  the sole  power to vote and  direct  the
disposition  of the securities  described  above,  for purposes of Reg.  Section
240.13d-3,  XAM may be deemed to  beneficially  own  1,685,596  shares of Common
Stock,  or  approximately  26.1% of the shares of Common Stock deemed issued and
outstanding as of November 4, 2004.







Item 1.   Security and Issuer.
          -------------------

          This statement relates to the common stock, par value $0.001 per share
(the "Common Stock"), of Aerogen, Inc., a Delaware corporation  (the "Company").
The Company has its principal  executive offices located at 2071 Stierlin Court,
Suite 100, Mountain View, California 94043.


Item 2.   Identity and Background.
          -----------------------

          The person filing this statement is Xmark Asset Management, LLC, a New
York limited liability company ("XAM").  XAM's business address is 152 West 57th
Street, 21st Floor, New York, New York 10019.

          XAM serves as the investment  manager for Xmark Fund, L.P., a Delaware
limited partnership ("Xmark LP") and Xmark Fund, Ltd., a Cayman Islands exempted
company  ("Xmark Ltd").  Xmark LP and Xmark Ltd are engaged in the investment in
personal  property of all kinds,  including  but not  limited to capital  stock,
depository  receipts,   investment  companies,   mutual  funds,   subscriptions,
warrants,  bonds,  notes,  debentures,  options and other securities of whatever
kind and nature.

          Mitchell  D.  Kaye,   whose  business   address  is  c/o  Xmark  Asset
Management,  LLC, 152 West 57th Street, 21st Floor, New York, New York 10019, is
the sole Manager of XAM.

          Neither of XAM nor Mr. Kaye has ever been  convicted  in any  criminal
proceeding  (excluding  traffic  violations  or similar  misdemeanors),  nor has
either XAM or Mr. Kaye been a party to any civil  proceeding  commenced before a
judicial or administrative  body of competent  jurisdiction as a result of which
XAM or Mr. Kaye,  respectively,  was or is now subject to a judgment,  decree or
final  order  enjoining  future  violations  of,  or  prohibiting  or  mandating
activities subject to, federal or state securities laws or finding any violation
with respect to such laws.

          Mr. Kaye is a citizen of the United States.


Item 3.   Source and Amount of Funds or Other Consideration.
          ------------------------------------------------- 

          The source of the funds used in making the  purchases of the Company's
securities described herein was working capital.


Item 4.   Purpose of Transaction.
          ---------------------- 

          As the beneficial owner of the percentage of the Company's outstanding
Common  Stock  described in Item 5 of the Schedule  13D, XAM can  influence  the
outcome  of  matters  that  may be  submitted  to  the  vote  of  the  Company's
stockholders  at annual or special  meetings  of  stockholders.  Such  corporate
actions may  include,  and are not limited to, the approval of each of the types
of actions  described  in (a) through  (g) of Item 4 of  Schedule  13D under the
Securities Exchange Act of 1934, or any similar actions.

          XAM also has the power to  influence  the  strategic  direction of the
Company as a result of  restrictive  covenants  contained in the  Certificate of





Designations  of the Series A-1 Preferred  Stock,  par value $0.001 per share of
the Company (the "Preferred  Stock") described in Item 6 of the Schedule 13D. In
addition,  under the terms of the Purchase Agreement  described in Item 6 of the
Schedule  13D,  Xmark  LP and  Xmark  Ltd  have the  right  (which  has not been
exercised to date) to designate two members to the Company's Board of Directors,
and to remove or replace their designees,  until they no longer collectively own
at least 80,000 shares of Preferred Stock in the aggregate.

          XAM may from time to time seek to utilize its voting and other  rights
to change or influence  control of, and to influence the  corporate  affairs of,
the Company,  including  through the use of its influence on the approval of any
of the events referred to above.

          XAM  intends  to  continue  to  evaluate  the  business  and  business
prospects of the Company and its present and future  interest in, and intentions
with respect to, the Company,  and in connection therewith may from time to time
consult with other stockholders of the Company.


Item 5.   Interest in Securities of the Issuer.
          ------------------------------------ 

          Based  on  information  reported  by the  Company  in  its  prospectus
relating to Registration  Statement No. 333-115813 filed with the Securities and
Exchange  Commission on August 17, 2004,  there were 4,784,506  shares of Common
Stock outstanding as of August 2, 2004.  As of November 4, 2004, Xmark LP is the
holder  of (i)  74,025  shares  (the  "Xmark  LP  Preferred")  of the  Company's
Preferred  Stock,  which are presently  convertible  into 740,250  shares of the
Company's Common Stock,  (ii) warrants expiring on March 22, 2009, which entitle
Xmark LP to purchase up to an aggregate of 339,600  shares of Common Stock at an
exercise  price of $3.25 per share (the "Xmark LP March 2009  Warrants"),  which
exercise  price is subject to adjustment as set forth in the Xmark LP March 2009
Warrants,  (iii)  warrants  expiring on May 11, 2009,  which entitle Xmark LP to
purchase up to an  aggregate  of 400,650  shares of Common  Stock at an exercise
price of $3.25 per share (the "Xmark LP May 2009  Warrants",  and together  with
the Xmark LP March 2009 Warrants, the "Xmark LP Warrants"), which exercise price
is subject to adjustment as set forth in the Xmark LP May 2009 Warrants and (iv)
8,411  shares of Common  Stock  issued in lieu of the cash  payment of quarterly
dividends on the Preferred Stock held  by Xmark LP for the quarters  ended March
31, 2004 and June 30, 2004.  As of November 4, 2004,  Xmark Ltd is the holder of
(i) 92,641  shares (the "Xmark Ltd  Preferred")  of Preferred  Stock,  which are
presently  convertible  into  926,410  shares of  Common  Stock,  (ii)  warrants
expiring  on March  22,  2009,  which  entitle  Xmark Ltd to  purchase  up to an
aggregate of 425,010  shares of Common  Stock at an exercise  price of $3.25 per
share (the "Xmark Ltd March 2009 Warrants"),  which exercise price is subject to
adjustment  as set forth in the Xmark Ltd March 2009  Warrants,  (iii)  warrants
expiring on May 11, 2009, which entitle Xmark Ltd to purchase up to an aggregate
of 501,400  shares of Common Stock at an exercise  price of $3.25 per share (the
"Xmark  Ltd May 2009  Warrants",  and  together  with the Xmark  Ltd March  2009
Warrants,  the  "Xmark  Ltd  Warrants"),  which  exercise  price is  subject  to
adjustment  as set  forth in the  Xmark Ltd May 2009  Warrants  and (iv)  10,525
shares of Common Stock issued in lieu of the cash payment of quarterly dividends
on the  Preferred  Stock held by Xmark Ltd for the quarters ended March 31, 2004
and June 30, 2004.

          The terms of the Xmark LP  Preferred,  the  Xmark Ltd  Preferred,  the
Xmark LP Warrants and the Xmark Ltd Warrants preclude each of Xmark LP and Xmark
Ltd from  converting  the Xmark LP  Preferred  and the Xmark  Ltd  Preferred  or
exercising the Xmark LP Warrants and the Xmark Ltd Warrants if the conversion or
exercise  thereof  would result in Xmark LP,  Xmark Ltd and/or their  affiliates





beneficially owning in excess of 4.99% of the Company's outstanding Common Stock
following any such conversion or exercise (the "Issuance Limitation"). Each such
Issuance  Limitation  is  waivable  by Xmark  LP and  Xmark  Ltd,  respectively,
providing 61 days' advance  written notice to the Company.  On November 3, 2004,
Xmark LP and Xmark Ltd each provided a written waiver of the Issuance Limitation
to the  Company  with  respect  to the  Xmark LP  Preferred  and the  Xmark  Ltd
Preferred.  As a result  of this  waiver  and as a result  of the fact  that XAM
possesses the sole power to vote and direct the  disposition  of the  securities
described above,  for purposes of Reg. Section  240.13d-3, XAM may  be deemed to
beneficially own 1,685,596 shares of Common Stock, or approximately 26.1% of the
shares of Common Stock deemed issued and outstanding as of November 4, 2004.

          During  the sixty  days  prior to  November  4,  2004,  there  were no
transactions in Common Stock, or securities convertible into, exercisable for or
exchangeable for Common Stock, by XAM or any person or entity  controlled by XAM
or any person or entity for which XAM  possesses  voting or  investment  control
over the securities thereof.


Item 6.   Contracts, Arrangements, Understandings or  Relationships With Respect
          to Securities of the Issuer.
          ----------------------------------------------------------------------

          Pursuant  to  the  terms  of  a  Purchase   Agreement  (the  "Purchase
Agreement"),  dated as of March 11, 2004, by and among the Company, Xmark LP and
Xmark Ltd, as Lead Investor,  and the other  investors set forth on Schedules I,
II and III thereto  (collectively,  the "Investors"),  the Company issued to the
Investors  1,142,094  shares of Preferred Stock and warrants (the "Warrants") to
purchase up to 11,249,390  shares of Common Stock at an exercise  price of $3.25
per share (the  "Financing").  The  Preferred  Stock is  convertible  into up to
11,420,940  shares of Common Stock at a conversion price of $3.00 per share. The
conversion  price of the Preferred  Stock and the exercise price of the Warrants
are each subject to adjustment upon the occurrence of certain events,  which may
result in an increase in the number of shares of Common Stock  issuable upon the
conversion of the Preferred Stock and the exercise of the Warrants.

          The Financing was effected through two closings. In the first closing,
on March 23, 2004,  the Company  issued  499,981  shares of Preferred  Stock and
warrants to purchase up to 4,999,810  shares of Common  Stock,  for an aggregate
cash purchase price of $14,999,430.  In the second closing, on May 12, 2004, (i)
the Company issued 589,881 shares of Preferred Stock and warrants to purchase up
to 5,898,810  shares of Common Stock,  for an aggregate  cash purchase  price of
$17,696,430 and (ii) SF Capital Partners,  Ltd. ("SF Capital") and the Carpenter
1983 Family Trust UA exchanged the outstanding  debentures  previously issued to
them by the Company for an aggregate of 52,232  shares of  Preferred  Stock.  SF
Capital also received a warrant to purchase up to 350,770 shares of Common Stock
at an exercise price of $3.25 per share in connection with its debt exchange.

          In  addition,  each holder of  Preferred  Stock is entitled to receive
cumulative  dividends in  preference  to any dividend on the Common Stock at the
rate of 6% of the  stated  value  per  share of the  Preferred  Stock,  which is
currently $30.00, paid quarterly in arrears on the first day of January,  April,
July and October in each year. Dividends may be paid, at the Company's election,
out of legally  available  funds or  through  the  issuance  of shares of Common
Stock. If dividends are paid in Common Stock, Xmark LP and Xmark Ltd may receive
additional shares of Common Stock.





          The terms of the Preferred  Stock and Warrants  preclude each Investor
from  converting  Preferred  Stock or exercising  Warrants if the  conversion or
exercise would result in the Investor and/or its affiliates  beneficially owning
in excess of 4.99% of the  Company's  outstanding  Common  Stock  following  the
conversion or exercise.  Each Investor can waive this  provision with respect to
the Preferred  Stock or Warrants it holds by providing 61 days' advance  written
notice to the Company.

          The holders of Preferred  Stock are entitled to vote together with the
holders of Common Stock as a single class. Each share of Preferred Stock has the
number of votes  equal to the  number of shares of Common  Stock into which such
share of Preferred Stock is convertible.

          In connection with the Financing, the Company, Xmark LP, Xmark Ltd and
the other Investors entered into a Registration  Rights  Agreement,  dated March
22,  2004,  pursuant  to  which  the  Company  agreed  to  prepare  and  file  a
registration  statement on Form S-3 with the Securities and Exchange  Commission
for the resale of the shares of Common Stock  issuable  upon  conversion  of the
Preferred Stock,  exercise of the Warrants as well as the shares of Common Stock
issuable as dividends on the Preferred  Stock in lieu of cash.  The Company also
agreed to perform  various  other  obligations  and  agreements  related to such
registration.

          Under the terms of the Purchase Agreement, Xmark LP and Xmark Ltd have
the right to designate two members to the Company's  Board of Directors,  and to
remove or replace  their  designees,  until they no longer  collectively  own at
least 80,000 shares of Preferred Stock in the aggregate.

          The  Certificate  of  Designations  of the  Preferred  Stock  contains
provisions  which, so long as at least two hundred thousand  (200,000) shares of
Preferred Stock are outstanding  (appropriately adjusted for any stock dividend,
split,  combination or other recapitalization), prohibit the Company from taking
certain material actions, such as, among other things,  amending its charter and
bylaws,  entering into a change in control transaction,  materially changing the
nature of the business, paying dividends, without the vote of (i) the holders of
at least a majority of the Preferred  Stock, and (ii) each of Xmark LP and Xmark
Ltd (so long as they  collectively own at least 80,000 shares of Preferred Stock
in  the  aggregate,  appropriately  adjusted  for  any  stock  dividend,  split,
combination or other recapitalization).

          In addition,  the  Certificate of  Designations of the Preferred Stock
provides  that so long as at least  two  hundred  thousand  (200,000)  shares of
Preferred Stock are outstanding  (appropriately adjusted for any stock dividend,
split, combination or other recapitalization), Xmark LP, Xmark Ltd and the other
Investors  have a right of first refusal in  connection  with any equity or debt
issuances  by the  Company  at any time  prior to March  23,  2005,  pro rata in
accordance with such Investor's Preferred Stock ownership.

          The  descriptions of the  transactions and agreements set forth in the
Schedule  13D are  qualified  in their  entirety by  reference  to the  complete
agreements  governing such matters,  each of which is  incorporated by reference
to the Schedule 13D as exhibits pursuant to Item 7 hereof.

          Except as otherwise  described  herein,  no  contracts,  arrangements,
understandings or similar  relationships exist with respect to the securities of
the Company between XAM and any person or entity.





Item 7.   Material to be Filed as Exhibits.
          --------------------------------

          1.  Purchase Agreement, dated as of March 11, 2004, by and between the
Company, Xmark LP, Xmark Ltd, and the other Investors, incorporated by reference
to Exhibit 10.24 to the Current Report on Form 8-K filed by the Company with the
Securities and Exchange Commission on March 26, 2004.

          2.  Certificate of Designations,  Preferences and Rights of Series A-1
Preferred Stock of the Company, dated March 19, 2004,  incorporated by reference
to Exhibit 10.25 to the Current Report on Form 8-K filed by the Company with the
Securities and Exchange Commission on March 26, 2004.

          3.  Form of Warrant, incorporated by reference to Exhibit 10.26 to the
Current Report on Form 8-K filed by the Company with the Securities and Exchange
Commission on March 26, 2004.

          4.  Registration Rights Agreement,  dated as of March 22, 2004, by and
between the Company and the  Investors,  incorporated  by  reference  to Exhibit
10.27 to the Current Report on Form 8-K filed by the Company with the Securities
and Exchange Commission on March 26, 2004.







                                    Signature
                                    ---------

          After reasonable inquiry and to the best of my knowledge and belief, I
certify that the information  set forth in this statement is true,  complete and
correct.


                                            As of November 4, 2004

                                            XMARK ASSET MANAGEMENT, LLC


                                            /s/ Mitchell D. Kaye 
                                            ------------------------------------
                                            Mitchell D. Kaye, Manager


Attention:  Intentional  misstatements  or omissions of fact constitute  Federal
criminal violations (See 18 U.S.C. 1001).