Six Indian geographical populations of D. dipectinata were analysed electrophoretically for allozymic variation at nine loci as well as for ethanol tolerance potential. Allelic frequency changes at Adh, Odh and Est-5 loci correlated significantly with increase in latitude. On the basis of FST values, Adh, Odh, Mdh and α-Gpdh loci depicted modest amounts of genetic differentiation. Thus, the occurrence of significant genotypic as well as allelic frequency heterogeneity, genic differentiation and clinal variation at polymorphic loci suggest evidence of natural selection maintaining such genic differentiation in D. bipectinata populations from the Indian sub-continent. The Indian populations of D. bipectinata revealed genetic differentiation in term of ethanol indices such as LT50hrs(72 to 96hrs), adult ethanol threshold concentration(2.5 to 4.0%), LC50 thanol concentration (2.7 to 4.2%). The parallel occurrence of latitudinal variation at Adh locus as well as ethanol tolerance in Indian geographical populations of D. bipectinata could be maintained by balancing natural selection varying spatially along the north south axis of the Indian sub-continent.