A new species of apogonid, Cercamia melanogaster, is described from 11 specimens, 17.1–28.0 mm SL, collected in 15–42 m in the Bird’s Head region of West Papua Province, Indonesia. Genetic evidence is provided to show a high level of divergence in the mtDNA COI marker between the three recognized species in Cercamia, including the new taxon, C. cladara, and C. eremia.