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For the first time, the analysis of polymorphism of complete mitochondrial genomes was performed in three Dagestan local goat populations (n = 37), which were characterized by high genetic and haplotype diversity. We found that 90.88% of the total genetic variability was due to intragroup differences and 4.86% was due to intergroup differences. For the studied sample of goats, significant negative values of the Tajima's D and Fu's Fs neutrality indices were calculated (P < 0.05). We performed a phylogenetic analysis using the nucleotide sequences of domestic goats and bezoars belonging to different haplogroups. Our study revealed that all studied samples of Dagestan Local goats belonged to haplogroup A, which is the most frequent one in domestic goats. [ABSTRACT FROM AUTHOR]