We describe a new species of Neotropical spiny-lizard of the genus Echinosaura from the Imbabura and Carchi Provinces on the western slopes of the Andes in northwestern Ecuador. The new species mostly resembles E. horrida. However, it can be distinguished from all congeners by having keeled enlarged dorsal scales forming a paired vertebral row, two paravertebral series of short oblique rows of projecting scales, and a pair of spine-like scales on temporal and nuchal regions. We also provide a detailed description of the osteology of the skull and pectoral girdle of the new species and present a phylogenetic hypothesis for Echinosaura based on three mitochondrial genes (12S, 16S, ND4) and one nuclear gene (c-mos).