Retinal homeobox (Rx/Rax) genes are essential for the organogenesis of the vertebrate eye. These genes are dynamically expressed in a tissue-specific manner during eye development, suggesting pleiotropic roles. We use a temporally-selective gene knockdown approach to identify endogenous functions for the zebrafish rx genes, rx1 and rx2. Depletion of rx1 over the period of eye organogenesis resulted in severely reduced proliferation of retinal progenitors, the loss of expression of the transcription factor pax6, delayed retinal neurogenesis, and extensive retinal cell death. In contrast, depletion of rx2 over the same developmental time resulted in reduced expression of pax6 in the eye anlage, but only modest effects on retinal cell survival. Knockdown of rx1 specifically during photoreceptor development inhibited the expression of multiple photoreceptor-specific genes, while knockdown of rx2 over this time selectively inhibited the expression of a subset of these genes. Our findings support a function for rx2 in regulating pax6 within the optic primordia, a function for rx1 in maintaining the pluripotent, retinal progenitor cell state during retinal development, as well as selective functions for rx1 and rx2 in regulating photoreceptor differentiation.