The genetic variability of honey bee populations, representing Apis mellifera macedonica, Apis mellifera cecropia and Apis mellifera carnica subspecies from the Balkan Peninsula countries of Bulgaria, Greece, Serbia and Montenegro, was studied using alloenzymic analysis of six enzyme systems (MDH-1, ME, EST-3, ALP, PGM and HK) corresponding to 6 loci. All loci were found to be polymorphic in most of the populations studied. The observed heterozygosity was found to range from 0.161 to 0.276. Allele frequencies of all loci were used to estimate Nei’s (1972) genetic distance, which was found to range between 0.001 and 0.101 among the populations studied. UPGMA and neighbour-joining phylogenetic trees obtained by genetic distance matrix methods show that the honey bee populations from Bulgaria and Greece were clustered together, as were those from Serbia and Montenegro.