Bactrocera cacuminata (Hering) is a nonpest member of the Bactrocera dorsalis complex offering a platform to check hypotheses extrapolated from the more studied pest species. Six polymorphic microsatellite loci were isolated from enriched genomic libraries constructed using a biotin/streptavidin capture protocol. Allele number varied between three and nine; the expected heterozygosity ranged between 0.29 and 0.81. No significant deviations from Hardy–Weinberg equilibrium or linkage disequilibrium were found. These microsatellite markers have potential to be used to examine population structure and mating systems in this tropical fruit fly.