Geographic and anthropogenic barriers can result in creating population structure in primates. We hypothesized that such features in the Northeast India could have given rise to subpopulations with variable genetic structure and diversity in Western Hoolock gibbons, Hoolock hoolock. For testing this, we collected faecal and blood samples from 37 individuals from H. hoolock spreading their whole distribution, isolated DNA, amplified mitochondrial markers and constructed a median joining network and measured gene flow between subpopulations from the data. We found high haplotype diversity in mitochondrial markers as well as presence of three sub-populations. Due to high diversity parameters, the population of Western hoolock gibbons in India seems healthy and resilient to changes. We expect that the results will assist in in-situ conservation of the species and in captive breeding programs in various zoos of the region. [ABSTRACT FROM AUTHOR]