Genetic variation of honey bee populations from 9 different locations of Bulgaria was studied using 4 enzymic systems (MDH, ME, EST and ALP) corresponding to 4 genetic loci and PCR-RFLP's analysis of 16s rDNA, COI, and ND5 gene segments of mtDNA. Allozyme analysis revealed that all loci were polymorphic in almost all studied populations. The observed heterozygosity was found to range from 0.146 to 0.258, and Nei's genetic distance between 0.006 and 0.057 among the populations. Bulgarian honey bees are clustered into three groups in neighbor-joining and UPGMA dendrograms. The Pomorie and Slivovik populations are in a separate clade while all other populations are grouped together. The mtDNA analyses revealed no variation in the Bulgarian honey bees.