Pangolins are under severe threat from illegal trade and habitat loss. Despite their conservation significance, these elusive creatures remain poorly understood, particularly in the context of phylogeography and genetic diversity. In this study DNA was isolated from two types of pangolin scat (faeces) samples (whole scat and swabs) which had been stored frozen for up to 3 years between the time of collection and our analyses. A mitochondrial sequence for the cytochrome b gene (424 bp) region was reliably generated from both sample types, for scats which appeared in ‘good’ or ‘poor’ condition at the time of collection. Sanger sequencing revealed four new cytochrome b haplotypes for pangolin, with variations in distinct sampling regions in Nepal (central and east). Comparison to reference sequences for pangolin originating from China, Taiwan and Thailand, indicated a distinct variant of Chinese pangolin in Nepal (15-19 base pair difference). Genetic differentiation of Chinese pangolin in Nepal has broader conservation significance for this species. Methods described here are robust and could be applied to broader genetic studies of pangolin populations across Nepal, allowing for genetic mapping of pangolin variations to assist in identifying populations of significance, evaluation of conservation interventions, and forensic applications supporting the fight against illegal poaching.