In the current study, the mitochondrial genes sequence for COI, Cyt b and 16s rRNA of seven species found in different parts of the world were retrieved from NCBI Gene Bank while, PCR products of COI, Cyt b and 16s rRNA genes obtained from C. lupus and C.aureus present in Pakistan were sequenced and aligned for comparison. The phylogenetic analysis of mitochondrial COI, Cyt b and 16s rRNA genes showed almost the same results for the extant species of genus Canis. 16s rRNA revealed C. latrans, C. lycaon and C. simensis showed close phylogenetic relation with each other. While, COI and Cyt b showed wider genetic distance. Cyt b and 16s rRNA analysis indicated C. mesomelas and C. adustus as sister taxa, while COI also proved the same phylogenetic association. COI and 16s rRNA revealed the least genetic distance between C. aureus and C. lycaon while Cyt b showed more genetic distance. COI, 16s rRNA analysis determined close phylogenetic relations between C. lupus and C. lycaon while Cyt b showed greater phylogenetic distinction between these two species. Cyt b and 16s rRNA revealed no genetic distance between C. latrans and C. lycaons while COI analysis identified both as genetically distant. Finally, COI, 16s rRNA successfully determined the phylogenetic association between C. aureus and C. adustus but Cyt b clarified more with higher genetic distance. Hence, it is concluded that 16s rRNA revealed least genetic distance while Cyt b showed higher genetic distances which suggest its potential use for species delineation especially for mammal.