Mitochondrial DNA (mtDNA) has been used extensively to study population genetics because it has the unique features of maternal inheritance, a relatively fast rate of evolution and lack of recombination. A total of 82 unrelated sheep from 10 Iranian indigenous sheep breeds were investigated to determinate the maternal genetic diversity using a sequence of a 685 bp segment of the displacement loop (D-loop) of mtDNA. Analysis of this region revealed 74 haplotypes and 123 polymorphic sites. Haplotype diversity, nucleotide diversity and the average number of nucleotide differences were estimated to be 0.996 ± 0.003, 0.0372 ± 0.0001 and 25.23, respectively. The sequence analysis also revealed high level of genetic diversity among the native Iranian breeds. Analysis of molecular variance revealed that 3.43 percent of the variation is found among populations compared with 96.57 percent variation found within populations. The Neighbor-Joining (NJ) tree indicated four (A, B, C and E) of the five haplogroups described so far are present in Iranian sheep breeds. The phylogenetic tree did not show any distinct genetic structure among the studied populations, which suggested that there existed strong gene flow and intermixing among sheep populations probably caused by extensive transportation of sheep in history and similar maternal lineages among the regions. پرونده مقاله