We describe a new sphaerodactylid lizard of the genus Gonatodes from the western flank of the Cordillera Oriental, Santander Department, Colombia based on morphological and molecular data. The new species is distinguished from all congeners by having a medium body size, by the absence of both a supraciliary spine and of clusters of distinctly enlarged conical scales on the sides and by having a subcaudal scale pattern (1’1”) and a cryptic dorsal color pattern in both sexes. Additionally, we describe for the first time the hemipenial morphology for a species of the genus. The new species increases the number of Gonatodes known from Colombia to eight and is the only known species of the country, as well as the second known mainland species of the genus not exhibiting sexual dichromatism.