| Summary: | <i>Maruca vitrata</i> is one of the primary biotic constraints for pigeon pea production in India. The present study assessed the genetic variation and population structure of <i>M. vitrata</i> from diverse agro-ecologies in India using the mitochondrial <i>cytochrome c oxidase</i> I gene. A low number of segregating sites (10), haplotypes (13), nucleotide diversity (0.00136), and overall mean genetic distance (0.0013) were observed among the populations. The negative values of the neutrality tests and unimodal mismatch distribution supported its demographic expansion in the country. The analysis of molecular variance (AMOVA) revealed that the variation among populations or groups was only 13.91%, and the geographical distance did not significantly contribute to the genetic differentiation (R<sup>2</sup> = 0.0024, <i>p</i> = 0.280). The clustering of haplotypes was also independent of the geographical location. Overall, our results suggest the existence of low genetic variation and high gene flow among populations of <i>M. vitrata</i> in India.
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