A photoreceptor is a specialized neuron that is responsible for the conversion of light into an electrical signal, which possess light-sensing ciliary organelles called outer segments. Peripherin 2 (PRPH2; also known as retinal degeneration slow protein, RDS), a photoreceptor-specific tetraspanin protein, is essential for the morphogenesis of the outer membranes and the visual function. A variety of the PRPH2 gene mutaions have been linked to a spectrum of hereditary retinal degenerative diseases. Recently, we have shown that the late endosome is the waystation that sorts newly synthesized PRPH2 to the cilium. We found that multiple C-terminal motifs of PRPH2 regulate its late endosome and ciliary targeting through ubiquitination and binding to Endosomal Sorting Complexes Required for Transport (ESCRT) component Hrs. Using the novel in vivo transfection system, we demonstrated that the entry of nascent PRPH2 into the outer segment could be blocked by its C-terminal mutations or by the expression of shRNA against Hrs. These findings shed light on a new biological role of the late endosomes in the biosynthetic pathway of ciliary proteins, and suggest that the late endosome can be a new therapeutic target for the diseases caused by ciliary defects.