A new species of the Gekko (Squamata: Gekkonidae) is described from the border of Sichuan and Yunnan Province, southwest China, based on distinct morphological and molecular features. Gekko jinjiangensis sp. nov. is distinguished from congeners by a combination of the following characters: size small (SVL 50.2–61.6 mm, n = 13); nares in contact with rostral; interorbital scales between anterior corners of the eyes 20–24; ventral scales between mental and cloacal slit 146–169; midbody scale rows 111–149; ventral scale rows 31–47; subdigital lamellae on first toe 8–11, on fourth toe 11–15; no webbing in the fingers and toes; with tubercles on uapper surface of fore and hind limbs; precloacal pores 4–5 in males; postcloacal unilateral tubercles 1–2; dorsal surface of body with 8–9 large greyish brown markings between nape and sacrum. In molecular analyses, the new species is sister to G. scabridus, but separated from them by approximately 9.9%–12.2% in genetic divergence as shown by a fragment of the partial mitochondrial ND2 gene. The new species is the highest Gekko with elevation range from 2000 to 2476 m. Further surveys are recommended to better understand the occurrence and population status of the new species.