Phylogenetics is a powerful tool for understanding the evolutionary history of organisms and for informing conservation and management of species. Among the strepsirrhine primates, the slender lorises are a threatened genus of small, nocturnal animals confined to India and Sri Lanka. The grey slender loris (Loris lydekkerianus) is divided into several subspecies based on the morphological and geographical variation but not supported by molecular data. We investigated the genetic basis of taxonomic and biogeographic variation as well as the phylogenetic divergence of two subspecies of the grey slender loris in southern India: the Mysore slender loris (Loris lydekkerianus ssp. lydekkerianus) and the Malabar slender loris (Loris lydekkerianus ssp. malabaricus). We sequenced and assembled the whole mitochondrial genomes of three representative individuals from their distribution in southern India and compared them with publicly available mitogenomes of other lorises. We found that the two Indian subspecies vary by 2.09% in the COX1 and CYTB gene regions and form distinct monophyletic clades that diverged about 1.049 million years ago. Our results support the morphological classification of these two subspecies in southern India and have implications for their conservation and management in captivity and in the wild.