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South American tomato leaf miner, (Meyrick, 1917) (Lepidoptera: Gelechiidae), is an important invasive pest of Tomato which invaded India and Nepal in 2014 and 2016, respectively. In the present study, samples from five localities of India and one from Nepal were used for the investigation of genetic diversity of by employing a fragment in the mtDNA gene-encoding cytochrome oxidase I (COI). Based on the partial COI gene, high genetic homogeneity was detected in populations of India and Nepal with rest of the world. Less nucleotide diversity ( 0.00137) was also detected in the populations of from different countries. This is first attempt to analyze molecular data for this new invasive species from India and Nepal.