<Page>

                                                             Exhibit 99.Cert.906

FORM N-CSR ITEM 10(b) EXHIBIT

                            CERTIFICATION PURSUANT TO
                             18 U.S.C. SECTION 1350,
                             AS ADOPTED PURSUANT TO
                  SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002

          The undersigned hereby certify in their capacity as Treasurer and
President, respectively, of EATON VANCE MUTUAL FUNDS TRUST (the "Trust") (on
behalf of Eaton Vance Tax-Managed Small-Cap Growth Fund 1.2), that:

   (a)  the Annual Report of the Trust (on behalf of Eaton Vance Tax-Managed
        Small-Cap Growth Fund 1.2) on Form N-CSR for the period ended October
        31, 2003 (the "Report") fully complies with the requirements of Section
        13(a) or 15(d) of the Securities Exchange Act of 1934, as amended; and

   (b)  the information contained in the Report fairly presents, in all material
        respects, the financial condition and the results of operations of the
        Trust (on behalf of Eaton Vance Tax-Managed Small-Cap Growth Fund 1.2)
        for such period.

A SIGNED ORIGINAL OF THIS WRITTEN STATEMENT REQUIRED BY SECTION 906 HAS BEEN
PROVIDED TO THE TRUST AND WILL BE RETAINED BY THE TRUST AND FURNISHED TO THE
SECURITIES AND EXCHANGE COMMISSION OR ITS STAFF UPON REQUEST.


EATON VANCE MUTUAL FUNDS TRUST (On behalf of Eaton Vance Tax-Managed Small-Cap
Growth Fund 1.2)

Date: December 16, 2003
      -----------------


/S/ James L. O'Connor
- ---------------------
James L. O'Connor
Treasurer

Date: December 16, 2003
      -----------------


/S/ Thomas E. Faust
- -------------------
Thomas E. Faust
President