Melanocytes and photosensory organs share a common ancestry that illuminates the origins of the neural crest.

In vertebrates, two major cell types produce extensive pigmentation: neuroepithelium-derived retinal pigment epithelium (RPE) of the eye and neural crest-derived melanocytes. Both produce melanin, express opsins, and exhibit photosensory functions. However, the evolutionary relationship between these cells - whether pigmentation was coopted or they share a common ancestry - remains unclear. We explore these scenarios including the hypothesis of a shared origin from an ancestral pigmented photosensory structure. For this, we harness single cell transcriptomics, chromatin accessibility and spatial transcriptomics data, to connect the transcriptional programs in melanocytes, pinealocytes and RPE with that of the pigmented cells in the sensory vesicle of the tunicate Ciona. The results reveal common regulatory gene expression modules spanning beyond pigment production, including photoreception, metabolism and biosynthesis. This evidence does not favor a model where pigmentation was coopted into one of these cell types, and rather supports the homology of melanocytes and RPE. Further, phylotranscriptomics approach expose recently-evolved melanocyte-specific and RPE-specific functions, which diversified after these types split from the ancestral cell type. Overall, our results support that melanocytes and RPE evolved from ancestral pigmented photosensory structures in chordates, initiating the origin of the neural crest - a major evolutionary driver of the vertebrate lineage.