Bothrocophias microphthalmus (Cope, 1875) currently comprises most mid- to highland populations of the genus Bothrocophias in the eastern versant of the Andes. We describe two new species of Bothrocophias from the highlands of the Colombian Andes previously referred to as B. microphthalmus based on morphological and genetic evidence. Our phylogenetic analysis revealed that B. micropthalmus as currently recognized is paraphyletic with respect to B. hyoprora , and the two new taxa are sister lineages. These new toadheaded pitvipers can be morphologically distinguished from their congeners based on the presence of contact between the internasal scales, the number of prefoveal scales, the presence of a lacunolabial scale, the arrangement of supralabial scales, ventral scale counts, the color pattern of the dorsal and ventral surfaces of the body and tail, and hemipenial morphology. We discuss some possible taxonomic scenarios for the lineages found within the B. microphthalmus species complex but refrain from making additional taxonomic changes given our reduced sampling of the southern lineages.