The highest elevations of the Tropical Andes form an archipelago of sky islands, where herpetological diversity is actively evolving. In this study, we combined morphological and molecular data to discover and describe a new snake species of the colubrid genus Tantilla from the middle-upper basin of the Boconó River on the lacustrine slope of the Cordillera de Mérida. This species belongs to the Tantilla melanocephala phenotypic group. Our results align with the previously published data, indicating that Andean populations diverged from a lowland ancestral lineage originating from the Guiana Shield and northern Brazil during the Miocene (~8 million years ago [Myr]). Morphologically, the new species is distinguished from the other members of the genus by its three longitudinal black stripes, the presence of two pale spots on the parietals instead of a pale nuchal band, noncontacting prefrontal and supralabial scales, the first pair of infralabial scales typically separated (rarely in contact), 138–145 ventral scales in males, <60 subcaudal scales in males, 12 maxillary teeth with a moderate diastema and an anterior process on the maxillary bone, and a unilobed, unicalyculate, and noncapitated hemipenis. We discuss the validity of certain available names and the zoogeographic patterns of Tantilla in its northernmost Andean distribution. Furthermore, our study provides the first evidence suggesting that Tantilla species richness may be underestimated in the mountainous regions of northern South America, where allopatric speciation driven by topographic complexity and niche conservatism has likely played a crucial role in the phenotypic and genotypic divergence of centipede snake populations.