Photoreceptors, the light sensors of the retina, come in two varieties: the light-sensitive rod photoreceptors, which are responsible for night vision, and the cone photoreceptors, which operate at higher light intensities and are responsible for daylight and color vision. These different tasks require specific morphological and molecular adaptations of rod and cone photoreceptors in the processes of transduction and transmission of light signals. Here we present the first deep proteome resource of mouse rod and cone photoreceptors to our knowledge. We have established a method using fluorescence-activated cell sorting (FACS) to isolate rod and cone photoreceptors that is compatible with downstream proteome analyses. Using cell type-specific markers, we confirmed the purity of our FACS strategy by RT-qPCR and quantitative MS. The proteomic data can be used to identify rod and cone photoreceptor-specific proteins and signaling pathways. For example, our data show that both photoreceptor types have the same SNARE complex components and major synaptic vesicle constituents, but differentially express the SNARE regulators Complexin 3 and Complexin 4. In another example, we integrated the rod and cone photoreceptor proteomes with data from a peptide-based affinity purification screen for retinal interactors of Complexin-SNARE complexes. In conclusion, we have developed a method for obtaining rod and cone photoreceptors suitable for protein analyses, providing a valuable resource for future studies.