We have studied mitochondrial (mt) DNA variation in 334 honey bee colonies from 7 different geographic regions of Turkey. We have evaluated Dra I restriction profiles of the CO-I CO-II intergenic region, Hinf-I and Taq-1 restriction profiles of the CO-I gene and EcoR-1 restriction profiles of the whole mtDNA. We obtained three different mtDNA patterns by EcoR-1 digestion. The pattern typical for A. m. carnica/A. m. ligustica predominated throughout Turkey (327 colonies, 97.9%). We observed the pattern common in African subspecies only in Hatay province (6 colonies, 1.8%) and a previously unreported pattern in one colony from Balikesir province (0.3%). Dra-1 restriction analysis of the CO-I CO-II intergenic region yielded seven haplotypes. Haplotype 1 (TrDra-1) was the most common one found in Turkey, whereas haplotype 2 (TrDra-2) was widely distributed in Eastern Anatolia. Based on mitochondrial ND2 sequences taken from two samples collected in each region, bees from Hatay clustered with A. m. lamarckii and A. m. meda (morphological A and O lineages), while bees from central Anatolia clustered within the C morphological lineage group.