Genetic diversity of a species is influenced by multiple factors, including theQuaternary glacial-interglacial cycles and geophysical barriers. Such factors are notyet well documented for fauna from the southern border of the Himalayan region.This study used mitochondrial DNA (mtDNA) sequences and ecological nichemodeling (ENM) to explore how the late Pleistocene climatic fluctuations andcomplex geography of the Himalayan region have shaped genetic diversity,population genetic structure, and demographic history of the Nepalese populationof Assam macaques (Macaca assamensis) in the Himalayan foothills. A total of 277fecal samples were collected from 39 wild troops over almost the entire distributionof the species in Nepal. The mtDNA fragment encompassing the complete controlregion (1121bp) was recovered from 208 samples, thus defining 54 haplotypes.Results showed low nucleotide diversity (0.0075± SD 0.0001) but high haplotypediversity (0.965± SD 0.004). The mtDNA sequences revealed a shallow populationgenetic structure with a moderate but statistically significant effect of isolation bydistance. Demographic history analyses using mtDNA sequences suggested a post-pleistocene population expansion. Paleodistribution reconstruction projected thatthe potential habitat of the Assam macaque was confined to the lower elevations ofcentral Nepal during the Last Glacial Maximum. With the onset of the Holoceneclimatic optimum, the glacial refugia population experienced eastward rangeexpansion to higher elevations. We conclude that the low genetic diversity andshallow population genetic structure of the Assam macaque population in the NepalHimalaya region are the consequence of recent demographic and spatial expansion.