Using nine microsatellite loci, the genetic diversity of natural populations of Bactrocera occipitalis and B. philippinensis was investigated. Estimates of genetic diversity based on allele number (na and ne), heterozygosity (Ho and He) and Shannon information index (I) revealed that the Cavite population was the most genetically diverse and Pangasinan was the least. AMong groups, the intermediates were the most genetically diverse and B. philippinensis was the least. A low level of genetic diversity was detected among populations and among groups. Pangasinan and Palawan were the most related while Palawan and Guimaras were the least. Among groups, B. occipitalis and intermediates were the most related while B. occipitalis and B. philippinensis were the elast. Dendrogram analysis indicated that B. occipitalis, B. philippinensis, and intermediates are not genetically distinct from each other.
