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Many taxa have independently evolved genetic sex determination where a single gene located on a sex chromosome controls gonadal differentiation. The gene anti-Mullerian hormone (amh) has convergently evolved as a sex determination gene in numerous vertebrate species, but how this gene has repeatedly evolved this novel function is not well understood. In the threespine stickleback (Gasterosteus aculeatus),amhwas duplicated onto the Y chromosome (amhy) ~22 million years ago. To determine whetheramhyis the primary sex determination gene, we used CRISPR/Cas9 and transgenesis to show thatamhyis necessary and sufficient for male sex determination, consistent with the function of a primary sex determination gene. We find thatamhycontributes to a higher total dosage ofamhearly in development and likely contributes to differential germ cell proliferation key to sex determination. The creation of sex-reversed lines also allowed us to investigate the genetic basis of secondary sex characteristics. Threespine stickleback have striking differences in behavior and morphology between sexes. Here we show one of the classic traits important for reproductive success, blue male nuptial coloration, is controlled by both sex-linked genetic factors as well as hormonal factors independent of sex chromosome genotype. This research establishes stickleback as a model to investigate howamhregulates gonadal development and how this gene repeatedly evolves novel function in sex determination. Analogous to the “Four Core Genotypes” model in house mice, sex-reversed threespine stickleback offer a new vertebrate model for investigating the separate contributions of gonadal sex and sex chromosomes to sexual dimorphism.