Phlebotomus (Phlebotomus) papatasi (Scopoli) collected in human dwellings from an agricultural villages Chaura, located in Gaya district, Bihar, India, showed morphological and anatomical variations. Male sand flies of this species exhibited variations in the genital structures, while females showed differences in the spermathecae and antenna segment three (A3). When the mitochondrial DNA of both male and female P. (P.) papatasi sensu lato population subjected to DNA barcoding, both the sexes of P. (P.) papatasi variants were found to be associated. The differences in the morphometric characteristics clearly constitutes preliminary evidence for infraspecific variation in P. (P.) papatasi s.l. population in India.