Adult flies from five taxa (Bactrocera carambolae Drew & Hancock (formerly ‘Malaysian A’), B. dorsalis (Hendel) sensu stricto, B. melastomatos Drew & Hancock, B. papayae Drew & Hancock (formerly ‘Malaysian B’) and B. propinqua (Hardy & Adachi) of the Bactrocera dorsalis complex were analysed at 17 enzyme loci using horizontal starch-gel electrophoresis. Eleven loci—aAdh, Ald, Gpd, Ldh, aMdh, cMdh, Me, Pgm, Pgd, Sod-F, Sod-S—were represented by the most common allele in the five taxa. Of these 11 loci, seven showed intraspecific variation in one or more taxa. Among the five taxa, B. melastomatos could be distinguished from the rest by two loci (Acp and Gpi), while B. propinqua could be separated by four loci (Acp, Est-D, Idh90, Pep-C). Bactrocera dorsalis, B. carambolae and B. papayae did not possess any species-characteristic locus/allele, but B. carambolae could be distinguished from the other two taxa by Idh. The proportion of polymorphic loci in the Malaysian taxa ranged from 0.41 to 0.53. Bactrocera propinqua had the lowest average heterozygosity (H=0.05), while that in B. carambolae, B. melastomatos and B. papayae ranged from 0.09 to 0.11. The genetic identity values indicate closest affinity between B. dorsalis and B. papayae (I=0.99), followed by B. caramboiae (I=0.92), B. melastomatos (I=0.84) and B. propinqua (I=0.69). Bactrocera melastomatos showed closest affinity to B. carambolae (I=0.87) and was most distant from B. propinqua (I=0.64).