In the current study, the mtDNA D-Loop region was analyzed in South Anatolian Red (SAR, n=51), Anatolian Black (NB, n=50), Anatolian Grey (AG, n=54), Native Southern Anatolian Yellow (NSAY, n=51), East Anatolian Red (EAR, n=54) and Zavot (ZAV, n=19) cattle breeds (n=279) to reveal diversity of mitochondrial DNA, differentiation of breeds, and relevance between genetic differentiations and geographic distributions. Blood samples were collected from native cattle breeds. Genomic DNA was isolated using a standard phenol/chloroform method. MtDNA D-loop region was amplified by PCR. After mtDNA sequence analysis, sequence of the D-Loop region was aligned with reference sequence. Haplotypes were determined and phylogenetic tree was constructed using BioEdit version 5.0.6, DNAsp version 5.10.01, MEGA 4.0 Network, Arlequin, Phylip and TreeView software. The sequence data was examined for nucleotide and haplotypes diversity, genetic distance between breeds visualized with Neighbor Joining tree and Median Joining Network, evaluated with mismatch distribution analyses, neutrality tests and AMOVA analyses. As a result in comparison with cattle breeds throughout the world, the higher nucleotide (π=0.02240, ±0.0005) and haplotype diversity (H=0.9966, ±0.0006) higher haplotype number and also high genetic variation within and between the populations were determined in native Anatolian cattle breeds. These findings support the idea that Anatolia has been situated in a central position during the domestication process of the cattle species.