The genetic diversity and phylogenetic structure was analyzed in Mahabadi goat population by mitochondrial DNA sequences. Phylogenetic analysis was carried out using hyper variable region 1 (896 bp) obtained form 30 animals. Mahabadi goat proved to be extremely diverse (average haplotype diversity of 0.999) and the nucleotide diversity values 0.022. A total of 30 Mahabadi goats were grouped into six haplotypes and the large majority of haplotypes were present in 15 animals. All Mahabadi haplotypes were classified into a haplogroup and revealed remarkably high genetic distances within the population when compared with other Asian goat populations, indicating high genetic variation in the Mahabadi goat. These results indicate high-divergence status of the Mahabadi goat and will influence breeding and conservation strategies adopted for this breed.