Red Junglefowl (RJF), the wild progenitor of modern day chicken (DC), are believed to be in genetic endangerment due to introgression of domestic genes through opportunistic matings with domestic or feral chickens. Previous studies from India reported rare hybridization of RJF in wild, however, RJF population structure,pattern of gene flow and their admixture with DC populations are poorly understood at the landscape level. We conducted this study with the large sample size, covering the predicted natural distribution range of RJF in India. We documented strong evidence of directional gene flow from DC to free ranging wild RJF, with the Northeast RJF population exhibiting the most genetic variants at nuclear & mitochondrial genome and indicated of being the ancestral population from which early radiation would have occurred. The results provide evidence that landscape features do not act as a barrier to gene flow and the distribution pattern could not be explored due to physical sharing or exchange of wild birds in the past when forests were continuous across RJF range in India.