Heterogenous landscape features of the Himalayan region shape the genetic structure of animal populations by delimiting spatial patterns of dispersal and reproduction. Integrating population genetic analysis with landscape features could yield results that shed light on the evolutionary diversity of the taxa therein. This study assessed the population genetic structure of the Nepal Himalayan langurs (Semnopithecus spp.) across almost their entire distribution range in the complex landscape of the Nepal Himalaya using the mitochondrial cytochrome b (CYTB, 1140 bp), cytochrome c oxidase I (COI, 676 bp), and control region (1088 bp) sequences. Sequences were successfully retrieved from 52 samples belonging to 17 troops of wild Himalayan langurs in Nepal. The concatenated alignment of the three loci (2904 bp) defined 35 unique haplotypes with haplotype and nucleotide diversities of 0.961 ± 0.017 and 0.0204 ± 0.004, respectively. The results of a median joining haplotype network and of inter-haplotypic phylogenetic analyses revealed five major clades across the country: one from the eastern, two from the central, and two from the western region of Nepal. No haplotypes were shared among the regions. The Mantel test results indicated that the landscape heterogeneity of the Himalaya has shaped the population genetic structure of the Himalayan langurs due to the combined effects of isolation by resistance and isolation by distance phenomena. The strong population genetic structure and deep mtDNA divergence warrants a detailed taxonomic assessment of the Himalayan langurs across their entire range. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.