FGF9 is a member of the fibroblast growth factor (FGF) family and is critical for early testicular development and germ cell survival in the mouse. <i>Fgf9</i> reinforces the testis determinant <i>Sox9</i> and antagonizes <i>Wnt4</i>, an ovarian factor. To determine whether <i>FGF9</i> has a conserved role in the mammalian gonad, we examined its expression in the gonads of a marsupial, the tammar wallaby <i>Macropus eugenii, </i>and compared it to <i>WNT4</i> expression. Marsupial <i>FGF9</i> is highly conserved with orthologues from eutherian mammals, including humans. FGF9 protein was detected in both the testis and ovary before sexual differentiation, but it subsequently became sexually dimorphic during the period of testicular differentiation. The protein was specifically enriched in the seminiferous cords of the developing testis in the Sertoli and germ cells. <i>FGF9</i> mRNA expression was upregulated in the tammar testis at the time of seminiferous cord formation and downregulated in the developing ovary in an opposite profile to that of marsupial <i>WNT4</i>. These observations suggest that <i>FGF9</i> promotes male fate in the early gonad of marsupials through an antagonistic relationship with <i>WNT4</i> as it does in eutherian mammals.