A new Gekko (subgenus Japonigekko) species, Gekko alpinussp. nov., is described from the Jinsha River Basin in southwestern China, between the border of Mangkang County, Xizang Autonomous Region and Batang County, Sichuan Province, according to the integrative taxonomic results combining molecular data and morphological characters obtained from the type series comprising 11 specimens. Our molecular phylogeny inferred from the mitochondrial 16S and ND2 gene fragments indicated that this new species is most closely related to Gekko jinjiangensis, but a considerable amount of genetic divergence exists between them (p-distance: 3.6%-4.1% (16S) and 7.1%–9.1% (ND2)). The new species can be distinguished from its congeners via a combination of series morphological characters. The discovery of this new species marks the highest altitudinal range (2400 to 2542 m a.s.l.) recorded for the subgenus Japonigekko and also represents a new provincial record for the genus in Xizang Autonomous Region.