<PAGE>

                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                  SCHEDULE 13G

                    Under the Securities Exchange Act of 1934

                                (Amendment No.          )*
                                               --------

                            Sangamo Biosciences, Inc.
                                (Name of Issuer)

                                  Common Stock
                         (Title of Class of Securities)

                                    800677106
                                 (CUSIP Number)

                                December 31, 2003
             (Date of Event Which Requires Filing of this Statement)

     Check the appropriate box to designate the rule pursuant to which this
                               Schedule is filed:

                                [x] Rule 13d-1(b)

                                [ ] Rule 13d-1(c)

                                [ ] Rule 13d-1(d)

*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 the
disclosures provided in a prior cover page.

The information required in 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).

                               Page 1 of 10 pages


<PAGE>

-------------------                                           ------------------
CUSIP No. 800677106               13G                         Page 2 of 10 Pages
-------------------                                           ------------------

--------------------------------------------------------------------------------
1    NAME OF REPORTING PERSON
     S.S. or I.R.S. IDENTIFICATION NO. OF ABOVE PERSON

        Columbia Wanger Asset Management, L.P. 36-3820584

--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*

        Not Applicable                                                   (a) [ ]
                                                                         (b) [ ]

--------------------------------------------------------------------------------
3    SEC USE ONLY

--------------------------------------------------------------------------------
4    CITIZENSHIP OR PLACE OF ORGANIZATION

        Delaware

--------------------------------------------------------------------------------
       NUMBER OF    5    SOLE VOTING POWER

                            None
        SHARES
                    ------------------------------------------------------------
     BENEFICIALLY   6    SHARED VOTING POWER

                            1,700,000

       OWNED BY
                    ------------------------------------------------------------
                    7    SOLE DISPOSITIVE POWER
         EACH
                            None
       REPORTING
                    ------------------------------------------------------------
                    8    SHARED DISPOSITIVE POWER
      PERSON WITH
                            1,700,000

--------------------------------------------------------------------------------
9    AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

        1,700,000

--------------------------------------------------------------------------------
10   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*

        Not Applicable                                                       [ ]

--------------------------------------------------------------------------------
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

        6.9 %

--------------------------------------------------------------------------------
12   TYPE OF REPORTING PERSON*

        IA

--------------------------------------------------------------------------------


<PAGE>

-------------------                                           ------------------
CUSIP No. 800677106               13G                         Page 3 of 10 Pages
-------------------                                           ------------------

--------------------------------------------------------------------------------
1    NAME OF REPORTING PERSON
     S.S. or I.R.S. IDENTIFICATION NO. OF ABOVE PERSON

        WAM Acquisition GP, Inc.

--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*

        Not Applicable                                                   (a) [ ]
                                                                         (b) [ ]

--------------------------------------------------------------------------------
3    SEC USE ONLY

--------------------------------------------------------------------------------
4    CITIZENSHIP OR PLACE OF ORGANIZATION

        Delaware

--------------------------------------------------------------------------------
       NUMBER OF    5    SOLE VOTING POWER

                            None
        SHARES
                    ------------------------------------------------------------
     BENEFICIALLY   6    SHARED VOTING POWER

                            1,700,000

       OWNED BY
                    ------------------------------------------------------------
                    7    SOLE DISPOSITIVE POWER
         EACH
                            None
       REPORTING
                    ------------------------------------------------------------
                    8    SHARED DISPOSITIVE POWER
      PERSON WITH
                            1,700,000

--------------------------------------------------------------------------------
9    AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

        1,700,000

--------------------------------------------------------------------------------
10   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*

        Not Applicable                                                       [ ]

--------------------------------------------------------------------------------
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

        6.9 %

--------------------------------------------------------------------------------
12   TYPE OF REPORTING PERSON*

        CO

--------------------------------------------------------------------------------


<PAGE>

-------------------                                           ------------------
CUSIP No. 800677106               13G                         Page 4 of 10 Pages
-------------------                                           ------------------

--------------------------------------------------------------------------------
1    NAME OF REPORTING PERSON
     S.S. or I.R.S. IDENTIFICATION NO. OF ABOVE PERSON

        Columbia Acorn Trust

--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*

        Not Applicable                                                   (a) [ ]
                                                                         (b) [ ]

--------------------------------------------------------------------------------
3    SEC USE ONLY

--------------------------------------------------------------------------------
4    CITIZENSHIP OR PLACE OF ORGANIZATION

        Massachusetts

--------------------------------------------------------------------------------
       NUMBER OF    5    SOLE VOTING POWER

                            None
        SHARES
                    ------------------------------------------------------------
     BENEFICIALLY   6    SHARED VOTING POWER

                            1,600,000

       OWNED BY
                    ------------------------------------------------------------
                    7    SOLE DISPOSITIVE POWER
         EACH
                            None
       REPORTING
                    ------------------------------------------------------------
                    8    SHARED DISPOSITIVE POWER
      PERSON WITH
                            1,600,000

--------------------------------------------------------------------------------
9    AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

        1,600,000

--------------------------------------------------------------------------------
10   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*

        Not Applicable                                                       [ ]

--------------------------------------------------------------------------------
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

        6.4 %

--------------------------------------------------------------------------------
12   TYPE OF REPORTING PERSON*

        IV

--------------------------------------------------------------------------------


<PAGE>

Item 1(a) Name of Issuer:

               Sangamo Biosciences, Inc.

Item 1(b) Address of Issuer's Principal Executive Offices:

               501 Canal Blvd., Suite A100
               Richmond, California 94804

Item 2(a) Name of Person Filing:

               Columbia Wanger Asset Management, L.P. ("WAM")
               WAM Acquisition GP, Inc., the general partner of WAM
               ("WAM GP")
               Columbia Acorn Trust ("Acorn")

Item 2(b) Address of Principal Business Office:

               WAM, WAM GP, and Acorn are all located at:

               227 West Monroe Street, Suite 3000
               Chicago, Illinois 60606

Item 2(c) Citizenship:

               WAM is a Delaware limited partnership; WAM
               GP is a Delaware corporation; and Acorn is a
               Massachusetts business trust.

Item 2(d) Title of Class of Securities:

               Common Stock

Item 2(e) CUSIP Number:

               800677106

Item 3    Type of Person:

               (d)  Acorn is an Investment Company under section 8 of the
                    Investment Company Act.

               (e)  WAM is an Investment Adviser registered under section 203 of
                    the Investment Advisers Act of 1940; WAM GP is the General
                    Partner of the Investment Adviser.

                               Page 5 of 10 pages


<PAGE>

Item 4    Ownership (at December 31, 2003):

               (a)  Amount owned "beneficially" within the meaning of rule
                    13d-3:

                    1,700,000

               (b)  Percent of class:

                    6.9 % (based on 24,814,486 shares outstanding as of
                    September 30, 2003)

               (c)  Number of shares as to which such person has:

                         (i)  sole power to vote or to direct the vote:
                              none

                         (ii) shared power to vote or to direct the vote:
                              1,700,000

                         (iii) sole power to dispose or to direct the
                              disposition of: none

                         (iv) shared power to dispose or to direct
                              disposition of: 1,700,000

Item 5    Ownership of Five Percent or Less of a Class:

               Not Applicable

Item 6    Ownership of More than Five Percent on Behalf of Another Person:

               The shares reported herein have been acquired on behalf of
               discretionary clients of WAM, including Acorn. Persons other than
               WAM and WAM GP are entitled to receive all dividends from, and
               proceeds from the sale of, those shares. Acorn is the only such
               person known to be entitled to all dividends from, and all
               proceeds from the sale of, shares reported herein to the extent
               of more than 5% of the class.

Item 7    Identification and Classification of the Subsidiary Which Acquired the
          Security Being Reported on by the Parent Holding Company:

               Not Applicable

Item 8    Identification and Classification of Members of the Group:

               Not Applicable

Item 9    Notice of Dissolution of Group:

               Not Applicable

                               Page 6 of 10 pages


<PAGE>

Item 10   Certification:

               By signing below I certify that, to the best of my knowledge and
          belief, the securities referred to above were acquired and are held in
          the ordinary course of business and were not acquired and are not held
          for the purpose of or with the effect of changing or influencing the
          control of the issuer of the securities and were not acquired and are
          not held in connection with or as a participant in any transaction
          having that purpose or effect.

                               Page 7 of 10 pages


<PAGE>

                                    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.

Date: February 13, 2004

               The undersigned corporation, on the date above written, agrees
               and consents to the joint filing on its behalf of this Schedule
               13G in connection with its beneficial ownership of the security
               reported herein.

                                    WAM Acquisition GP, Inc.
                                        for itself and as general partner of
                                        COLUMBIA WANGER ASSET MANAGEMENT, L.P.


                                    By: /s/ Bruce H. Lauer
                                        ----------------------------------------
                                            Bruce H. Lauer
                                            Senior Vice President and Secretary

               The undersigned trust, on the date above written, agrees and
               consents to the joint filing on its behalf of this Schedule 13G
               in connection with its beneficial ownership of the security
               reported herein.

                                    COLUMBIA ACORN TRUST


                                    By: /s/ Bruce H. Lauer
                                        ----------------------------------------
                                            Bruce H. Lauer
                                            Vice President, Treasurer and
                                            Secretary

                               Page 8 of 10 pages


<PAGE>

                                  Exhibit Index

Exhibit 1 Joint Filing Agreement dated as of February 13, 2004 by and among
          Columbia Wanger Asset Management, L.P., WAM Acquisition GP, Inc., and
          Columbia Acorn Trust.

                               Page 9 of 10 pages


<PAGE>

                                                                       EXHIBIT 1

                             JOINT FILING AGREEMENT

     The undersigned hereby agree to the joint filing of the Schedule 13G to
which this Agreement is attached.

               Dated: February 13, 2004

                                    WAM Acquisition GP, Inc.
                                        for itself and as general partner of
                                        COLUMBIA WANGER ASSET MANAGEMENT, L.P.


                                    By: /s/ Bruce H. Lauer
                                        ----------------------------------------
                                            Bruce H. Lauer
                                            Senior Vice President and Secretary


                                    COLUMBIA ACORN TRUST


                                    By: /s/ Bruce H. Lauer
                                        ----------------------------------------
                                            Bruce H. Lauer
                                            Vice President, Treasurer and
                                            Secretary

                              Page 10 of 10 pages