Bactrocera cucurbitae (Coquillett) is an important insect pest of melon fruit causing extensive losses of production in Asia and Pacific areas. Twelve polymorphic microsatellite loci were isolated from an enriched DNA library of this species and their amplification characteristics are described. Genetic parameters were estimated on 80 individual flies from four natural populations. Allele numbers per locus ranged from three to 20. These microsatellite markers have potential utility in population structure and gene flow studies of B. cucurbitae.