The phylogenetic relationships and biogeography of the Asiatic orchid genus Holcoglossum (Vandeae, Aeridinae) were inferred from sequences of chloroplast matK and trnL-F genes and nuclear ITS regions of 25 taxa. (12 Holcoglossum, 11 Aeridinae, 2 outgroups). Analysis of combined datasets with parsimony and Bayesian methods revealed that Holcoglossum is highly Supported as monophyletic, including two debatable species, H. amesianum and H. subulifolium, and consists of three well-supported major subclades which agree well with biodiversity centers of Holcoglossum: one tropical subclade comprising four species, another forming a polytomy comprising six species restricted to the temperate alpine region of the Hengduan Mountains, and the third with two species somewhat distributed between the first two regions. However, these three major subclades are only partly in accordance with previous infrageneric classifications based on morphological characters. The lip lamella, long and conical spur and tapering stipe seem to have evolved at least twice in Holcoglossum, similarly the pollination system shift has occurred at least twice. Vicariance analyses and molecular phylogeny suggest that Holcoglossum dispersed from tropical regions to the Hengduan Mountains and then radiated there as a result of the uplift of Qinghai-Tibetan Plateau.