Gonadogenesis, the process of forming an ovary or a testis from a bipotential gonad, is critical to the development of sexually-reproducing adults. While the molecular pathway underlying vertebrate gonadogenesis is well-characterized in organisms exhibiting genotypic sex determination, it is less well understood in vertebrates whose sex is determined by environmental factors. We examine the response of six candidate sex-determining genes to sex-reversing temperature shifts in a species with temperature-dependent sex determination (TSD). For the first time we report the regulation of FoxL2, Wnt4, Dmrt1 and Mis by temperature, confirming their involvement in the molecular pathway underlying TSD and placing them downstream of the action of temperature. We find evidence that FoxL2 plays an ovarian-specific role in development, while Wnt4 appears to be involved in both testis and ovary formation. Dmrt1 expression shows rapid activation in response to a shift to male-producing temperature, while Mis upregulation is delayed. Further, early repression of Mis appears critical to ovarian development. We also investigate Dax1 and Sox9 and reveal that at the level of gene expression, response to temperature is comparatively later in gonadogenesis. By examining the role of these genes in TSD, we can begin to elucidate elements of conservation and divergence between sex-determining mechanisms.