Morphological and isozyme analyses were used to determine if there were differences among groups of Bactrocera spp. collected from Guimaras Island and Laguna, Philippines. Each population was divided into seven groups based on six morphological criteria. Morphological analysis of aedeagus/aculeus length and wing cell diameter showed that these characteristics did not differ considerably among the groups. Isozyme analysis revealed eight presumptive loci coding for three enzymes. Acid phosphatase (ACP) and esterase (EST) had three loci each, while alkaline phosphatase (ALP) had two. Two alleles, S and F, were found for ACP-1, ACP-3, EST-1, ALP-1 and ALP-2. ACP-2 and EST-3 showed one allele, S, while EST-2 showed three S, M and F. Generally, the groups of Bactrocera spp. from Guimaras Island had higher genetic variation than those from Laguna. For both locations, however, intrapopulation variation was generally higher in groups 0, 1 and 2 (presumed to be B. occipitalis) than in groups 3 and 4 (presumed to be "hybrids"). Estimates of interpopulation variation showed the presence of considerable variation among the groups. Genetic differences were generally higher between groups from the opposite ends of the classification scheme. In Laguna, groups 0 and 2 with genetic identity I(N) = 0.8271 and genetic distance D = 0.1898 were the most genetically similar while groups 1 and 5 were the most genetically different (I = 0.2456; D = 1.4040). In Guimaras, groups 2 and 4 were the most genetically similar (I = 0.8580, D = 0.1532) while groups 2 and 6 were the most genetically different (I = 0.3211; D = 1.136). The morphological data did not conform with the isozyme data for the eight presumptive loci.
