We describe 15 polymorphic dinucleotide microsatellite loci in the black-and-gold chromis, Neoglyphidodon nigroris (Cuvier: Teleostei: Pomacentridae). Microsatellites were isolated from a partial genomic library that was enriched for CA repeat motifs. The 15 loci yielded between two and 23 alleles per locus in a sample of 16 fish from two forereef sites off the island of Hoga, Wakatobi National Park, Indonesia. Observed and expected heterozygosities varied from 0.13 to 1.00 and 0.24 to 0.98, respectively. These markers should allow us to discriminate between closely related individuals and also to assess the connectedness of populations of N. nigroris that inhabit different reefs.