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Tragulids hold a significant place in the evolutionary history of mammals since they represent the basal branch of ruminants. Only three genera of tragulids are being extant to date such as Tragulus, Hyemoschus and Moschiola. In the genus Moschiola, Sri Lankan chevrotains (Moschiola meminna and Moschiola kathygre) are endemic to Sri Lanka while Moschiola indica is present in India. Sri Lankan chevrotains lack information on their population structure, distribution and molecular evidence on species identification. This leads to possible threats including habitat destruction, poaching and illegal hunting and trading under different names. In this study, genomic DNA from hair follicles was isolated from M. meminna and M. kathygre and 12S rRNA mitochondrial gene was amplified using universal primers. The PCR products were sequenced and phylogenetic analysis was done on Sri Lankan chevrotains for the first time. The sequences of Sri Lankan chevrotains share 99.7% similarity as they differ only in a single InDel present in M. meminna. In silico analysis of 12S rRNA region revealed that PCR-RFLP approach can be used to differentiate the Sri Lankan chevrotains from Indian chevrotain using the restriction enzymes; Rsa I, Sca I, Hinf I and Hind III. M. kathygre and M. meminna can be differentiated from each other by using Dra I. [ABSTRACT FROM AUTHOR]