Nearly 6000 species of thrips have been described and only 12 species are reported to be vectors of tospoviruses (Bunyaviridae) globally In this regard, Thrips palmi and Scirtothrips dorsalis are two important vectors of Watermelon Bud Necrosis Virus (WBNV) and Peanut Yellow Spot Virus (PYSV) to watermelon and groundnut respectively in India. Accurate and timely identification of thrips vectors in the early developmental stages is important for understanding the epidemiology of tospoviruses, their management and also in quarantine. Morphological identification of thrips often has been a stumbling block in the absence of trained personnel. Using the tools of molecular biology, morphological identification is further strengthened by developing species-specific markers, which can differentiate the above two species of thrips based on the PCR amplicon size. Molecular studies can elucidate the occurrence of biotypes or cryptic species, if any. In this study, we examined genetic differences in COI among 21 populations of T. palmi collected from Karnataka, India, along with the sequences from other countries which were acquired from GenBank. The phylogenetic analysis showed that there are two major groups: one is clearly associated with Indian population of T. palmi and the second is associated with the remaining countries (Japan, Thailand, Dominican Republic, China, and U.K.). Our studies clearly refute the general belief that T. palmi is a single cosmopolitan and polyphagous species. On the contrary, by the standards of genetic and ecological differentiation in other species groups, the recognition of geographically associated and distinct T. palmi subspecies may be considered, similar to what has been observed in T. tabaci. Such similar results have been observed for S. dorsalis, where Indian and Chinese population of S. dorsalis form separate groups.