Trachypithecus, which currently contains 20 species divided into four groups, is the most speciose and geographically dispersed genus among Asian colobines. Despite several morphological and molecular studies, however, its evolutionary history and phylogeography remain poorly understood. Phayre’s langur (
Trachypithecus phayrei) is one of the most widespread members of the genus, but details on its actual distribution and intraspecific taxonomy are limited and controversial. Thus, to elucidate the evolutionary history of
Trachypithecus and to clarify the intraspecific taxonomy and distribution of
T. phayrei, we sequenced 41 mitochondrial genomes from georeferenced fecal samples and museum specimens, including two holotypes. Phylogenetic analyses revealed a robustly supported phylogeny of
Trachypithecus, suggesting that the
T. pileatus
group branched first, followed by the
T. francoisi group
, and the
T. cristatus
and
T. obscurus
groups most recently. The four species groups diverged from each other 4.5–3.1 million years ago (Ma), while speciation events within these groups occurred much more recently (1.6–0.3 Ma). Within
T. phayrei, we found three clades that diverged 1.0–0.9 Ma, indicating the existence of three rather than two taxa. Following the phylogenetic species concept and based on genetic, morphological, and ecological differences, we elevate the
T. phayrei subspecies to species level, describe a new species from central Myanmar, and refine the distribution of the three taxa. Overall, our study highlights the importance of museum specimens and provides new insights not only into the evolutionary history of
T. phayrei but the entire
Trachypithecus genus as well.
