Taxonomic rank of terrestrial tortoise inhabiting in India and adjacent countries has been an unresolved issue. Wild living species of Manouria and Indotestudo genera have been classiied through conventional taxonomy, but not adequately discriminated by mitochondrial cytochrome b gene. Cytochrome oxidase (COI) marker has been quite successful to achieve the exact species level information. There needs of an accurate sequence based effort for the extant northeast (NE) Indian tortoises to identify them accurately and to provide locality information. To estimate the Kimura-2-Parameter (K2P) divergences and to construct the NeighbourJoining (NJ) phylogeny, we generated six partial COI sequences derived from expert-identiied tortoise specimens. Both BLASTn and Bold-IDs revealed the deinitive identity of Manouria, whereas the congeners of Indotestudo remain inconclusive by only a two-fold interspeciic divergence gap with the other named Indian tortoise species. The NJ phylogeny readily differentiated the three Indian tortoise genera with their respective conspecies but depicted a nonsynonomous group of Indotestudo congeners. This study shows that the molecular identiication of Manouria emys phayrei, Indotestudo elongata and an allopatric population of Indotestudo forstenii in NE India corresponds correctly with existing morphological key support.