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. Diagnostic features include dorsal rays VI-I,9; anal rays II,11–13; pectoral rays 9–11; gill rakers 1 + 10–12; scales cycloid, about 22–23 in lateral series and 9–10 in transverse series; scales present on preopercle and opercle; colour overall transparent pinkish with broad red zone on side of snout to rear margin of head, red on ventralmost part of head, and dark brown (nearly black) abdomen with diagonal pearly white band from upper rear margin of operculum to vent. 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.