Synaptojanin 1 (SynJ1) is a polyphosphoinositide phosphatase involved in clathrin-mediated endocytosis in conventional synapses. Studies with the zebrafish mutant nrc have revealed that loss of SynJ1 also affects cone photoreceptor ribbon synapses, causing pronounced morphological and functional abnormalities. In this study we continue to examine the role of SynJ1 in photoreceptors. Using a newly generated antibody specific for zebrafish SynJ1, we localized this protein predominantly to cone photoreceptors. We then used blastula stage transplantation experiments to demonstrate that rods from nrc mutants lacking SynJ1 develop normally and do not have the pronounced morphological defects detected in cones. Given the known involvement of SynJ1 in synaptic vesicle endocytosis, we hypothesize that rods and cones use distinct mechanisms for vesicle recycling.