We have developed seven microsatellite markers from an enrichment library of genomic DNA for an endangered species, Morus boninensis. A total of 112 of the 320 clones were found to have unique sequences with microsatellite repeats. Seven of 54 primer pairs revealed clear chromatograms and polymorphisms among 36 individuals sampled from three of the Bonin Islands. Seven to 17 alleles per locus were detected, and the expected heterozygosity without considering double reduction ranged from 0.429 to 0.819. These findings should be useful for those studying the conservation genetics of M. boninensis.