This study presents a comprehensive morphological comparison along with molecular phylogeny of the genus Gloydius based on five mitochondrial genes (12S, 16S, COI, cytb, and ND4). The specimens collected from Jiuzhaigou National Nature Reserve are shown to be a new species, Gloydius lateralissp. nov. Zhang, Shi, Jiang & Shi based on a combination of morphological and molecular accounts. G. lateralissp. nov. differs from other congeneric species by a series of diagnostic morphological characteristics and forms a strongly supported monophyletic group. The new species is phylogenetically closely related to G. swild, another recently described species from Heishui, Aba, Sichuan.