Forty five natural populations of Drosophila ananassae, collected from entire geo-climatic regions of the India were analyzed to determine the distribution of genetic diversity relative to different eco-geographic factors. Quantitative data on the frequencies of three cosmopolitan inversions in the sampled populations were utilized to deduce Nei’s gene diversity estimates. Populations were grouped according to the time of collection (years and month); collection-regions like coastal and mainland regions, and collection-seasons. Further, data was subjected to network analysis to detect community structure in the populations and Modularity analysis to quantify the strength in community structure. Gene-diversity statistics revealed the presence of significant variability in the Indian natural populations of D.ananassae. Off all the parameters used to group the populations, geographical attributes seems to have maximum, while the time of collection and seasons have minimum influence on the genetic variability in Indian natural populations of D.ananassae. The results clearly link the association of genetic variability with environmental heterogeneity, elucidating the role of environment specific natural selection. The homogenizing effects could be due to genetic hitchhiking and canalization.