CRISPR technology has enabled interrogation of gene’s function in high-throughput manner. We conducted a genome-wide CRISPR-Cas9 screen to identify genes involved in melanin production in human skin pigment cells. In follow-up studies, by combining transcriptomic and organelle level proteomics, we investigated a novel role of Commander complex proteins in human melanogenesis. Together, our work expands the genes involved in melanin production that could be potential targeted for modulating melanin levels for biomedical applications.