The biodiversity of Yunnan, which is located in the Hengduan Mountains region of South-west China, is still underestimated. Here, we explore species diversity of Asian green pitvipers occurring in this region. Based on four mtDNA gene fragments (cyt. b, ND4, 12S RNA, and 16S RNA), we inferred phylogenetic position and relationships of Yunnan green pitvipers using Bayesian Inference (BI) and Maximum Likelihood (ML) methods. Both methods consistently revealed that all examined Yunnan specimens are placed in five clades which should be referred to Trimeresurus albolabris, Viridovipera stejnegeri, V. gumprechti, and the genus Popeia, respectively. It was unexpected that the samples allied to V. gumprechti did not form a monophyletic clade, but rather two well supported, distinct clades. Further morphological comparison suggested that the specimens nested within the clade Popeia should be identified as P. popeiorum, which is a species new to China. As a result, there are currently at least five species occurring in Yunnan, China: Trimeresurus albolabris, Viridovipera stejnegeri, V. yunnanensis, V. gumprechti, and Popeia popeiorum.