In this study, the genetic structure of Turkish honey bee (Apis mellifera L.) populations, mainly obtained from the Central Anatolian region, were investigated at three different mitochondrial regions. A total of 165 worker bees were collected from 15 different populations in ten different locations. Portions of the mitochondrial 16S ribosomal RNA (16S rDNA), cytochrome C oxidase I (COI) and NADH dehydrogenase 5 (ND5) genes were amplified by PCR and then subjected to RFLP pattern analysis using 18 restriction enzymes (these having at least one recognition site in each region were used). Nucleotide polymorphisms were revealed using restriction enzymes Bsp1431, DraI and SspI in 16S rDNA and TaqI in the COI gene segment. The polymorphisms were subsequently confirmed by direct DNA sequencing with sequences thereafter deposited in Genbank. In this study, six novel composite genotypes (haplotypes) were found in Turkish honey bee populations. The most common haplotype, type 1, was found in 12 of the sampled populations and overall accounted for 85.5% of the samples. TCS spanning network of haplotypes revealed that type 1 was the basal haplotype. Genetic distance (D) values were found to be low (0.0-0.0112) within Turkish honey bee populations. The average haplotype diversity (h) within populations was 0.082. Molecular phylogenetic analysis revealed that Konya/Sizma, Antalya/Elmali and Konya/Selcuklu populations were the most distant from all the other Turkish honey bee populations surveyed.