To identify the evolutionary lineage of honey bee colonies in Turkey, the mtDNA of 244 colonies from 20 locations was analyzed. Several polymorphic restriction sites showed that they belonged to the Mediterranean C lineage. DraI digestion of the CoxI-CoxII intergenic region produced four fragment patterns, one first seen in this study. From 37 colonies from 16 different locations in Turkey and two colonies from Iran, the intergenic region was sequenced. Previously, from among all honey bee populations of the C lineage, eight haplotypes had been described from this mtDNA region, three of which were found here. In addition, eight new haplotypes were found. A deletion in one of these haplotypes accounts for the novel DraI RFLP pattern. Most of the novel haplotypes were in a subgroup of lineage C, yet none of these had been found in previous studies of Turkish honey bees. The geographical distribution of some haplotypes suggests that they may be characteristic of subspecies native to Turkey.