Eggplant fruit and shoot borer or EFSB (Leucinodes orbonalis Guenee (Lepidoptera: Pyralidae)) is a destructive pest of eggplant (Solanum melongena) in the Asian subcontinent and Southeast Asia. There is limited information on the nature and extent of genetic diversity in this pest.Amplified fragment length polymorphism-polymerase chain reaction (AFLP-PCR) analysis was used to characterize 29 natural populations from different eggplant growing regions of India. Forty primer combinations were screened initially, of which 15 primer pairs were selected based on the band resolution and PCR reproducibility. The fifteen primer combinations generated AFLP patterns with fragments ranging from 25-60 fragments per primer pair depending on the populations screened and the number and nature of the selective nucleotides used. Data analysis is in progress to determine the extent of inter- and intra- population variability amongst the different individuals of the populations. The results reported in this study demonstrate the utility of AFLP in generating markers useful for genetic analysis in EFSB populations. This report is the first detailed genetic diversity analysis study of EFSB, which is economically the most significant pest of eggplant in India.