Abstract Owing to the harsh terrain, few biodiversity surveys have been carried out in the Pan-Himalaya Region. Among the understudied taxa from this region, Jerdon’s forest lizard, Calotes jerdoni, is believed to have a wide distribution, from northeast India to southwestern China. However, given the heterogeneous environment across its range and the lack of studies on this species, its taxonomy remains questionable. Using integrative taxonomic methods, we combined both morphological and genetic data from the type and topotypic specimens and examined the current taxonomic hypothesis of C. jerdoni across its range. Molecular data reveal that C. jerdoni as currently recognized, contains three deeply diverged lineages: one from the type locality in Northeast India, one from Western Myanmar, and another one from Southwestern China. The uncorrected genetic distances of mitochondrial coding gene ND2 among these three clades ranged over 10%. The Chinese population is sister to C. medogensis and paraphyletic to the remaining two clades of C. jerdoni. Morphological analyses confirm the results of the molecular analyses, where the Myanmar and Chinese populations can be diagnosed statistically in both univariate and multivariate space from the true C. jerdoni, as well as by a suite of reliable categorical morphological characters, including the size and shape of gular scales and ventral scales. To resolve the current taxonomic confusion, we resurrect the junior synonym, C. yunnanensis, for the Chinese population and expand its distribution to Myanmar, redescribe the elusive C. maria and C. medogensis based on its type material, and describe the remaining western Myanmar population as a new species. We further discuss the possibility of additional cryptic species within the complex in the Pan-Himalaya Region and provide a diagnostic key to all recognized members of the C. jerdoni complex.