Wild goat (Capra aegagrus), as an important and indicator species of mountainous regions of Iran has been confronted to population decline in recent years. So that, its conservation status classified as "Vulnerable" species. In present study, the phylogenetics relationships and genetic diversity of bezoar, based on polymorphism of D-loop region of mt-DNA has been investigated in three different habitats of Mazandaran Province; Kamarbon, Bandbon and Baladeh protected areas. The obtained phylogenetics trees show seven discrete clades and studied individuals of present study have the common ancestor and minimum two different origins for Mazandaran's Wild goats. As well, using Fst/1-Fst distance genetics matrix, the obtained NJ phylogeographic tree show the relationship between genetics and geography in three studied habitats and also with neighbor geographic areas. The results of genetic indicators such as Fu's Fs and Tajima's D show the mutation-genetic drift equilibrium in studied populations. On the other hand, regarding SSD and r factors amounts in Mismatch distribution analysis, the match of expected and observed amounts show the normality and expansion of the studied populations. The Analysis of Molecular Variation (AMOVA), regarding each haplogroup as one population show significant genetic difference between different clades of different haplogroups. Also, the high value of Fst indicator represents the significant genetic differentiation of different clades of wild goats.