Genetic differentiation among different natural populations of a species depends upon the environmental factors and the evolutionary forces that operate on them. In this study, seven Indian natural populations of D. bipectinata, two from north and five from south India, have been studied for their chromosomal inversion polymorphism. A total of nine paracentric autosomal inversions were recorded from these seven places but only three of them, present on the 2L, 2R and 3L were found to be cosmopolitan in distribution. In all the populations, the frequency of standard gene arrangement was found to be high than their respective cosmopolitan inversion gene arrangement. The average heterozygosity (Ho) of cosmopolitan inversions increases from north to south. There is a latitudinal cline in the distribution of three cosmopolitan inversion arrangements because their frequency increases with the decreasing latitude, i.e. from north to south India. A comparison of the genetic profile of two north Indian and five south Indian natural populations of D. bipectinata reveals the role of natural selection as well as bottleneck effect in the genetic structuring of these populations which may be due to their varying ecological conditions to which they are constantly encountered. Further, the presence of all kinds of paracentric inversions in individual populations was analysed following Poisson distribution to see whether these inversions occur randomly in natural populations or not and the results indicate that north Indian populations show the random occurrence of these inversions than the populations derived from the south.