We describe a new species of Macropholidus lizard from the Andean highlands of southern Ecuador and northern Peru based on recent collections. Among other characters, the new species differs from other species of Macropholidus in having a paired series of enlarged middorsal scale rows restricted to the nape, striated dorsal scales, as well as ocelli on tail, flanks, scapular region and neck. We also present a molecular phylogeny of Cercosaurinae and genetic distances as additional evidence supporting delimitation of the new species, which is sister to M. annectens from southern Ecuador. Data on Andean orogeny and age estimates of cercosaurine lizards suggest that the Huancabamba Depression, long recognized for its dual role as a biogeographic barrier and a migration corridor, has also served as a center of origin and diversification of Macropholidus lizards.