Legume pod borer, has lately emerged as one of the major insect pests of pigeonpea causing considerable crop losses. Thus, efficient management of is an important component for sustained pigeonpea productivity for which information on insect diversity could be useful. Present study was undertaken to evaluate the diversity in populations collected from major pigeonpea growing areas of India using molecular markers, () and - (-). Genomic DNA from larvae of different populations was extracted; 709 bp and 550 bp fragments of and - were PCR-amplified, cloned and sequenced. Comparison of sequences of different populations using multiple sequence alignment did not show any differences in and - sequences within the Indian populations. However, further analysis based upon sequences has revealed moderate nucleotide diversity ( = 0.26174) among Indian and global populations, whereas nucleotide diversity within Indian populations is nonsignificant ( = 0.00226). Additionally, phylogenetic analysis of sequences grouped all the Indian populations into one cluster while that of global were completely separate indicating a different ancestral background. This is a maiden attempt for diversity assessment of Indian populations that established them to be genetic homologs with different ancestral background.