Coendou quichua is a widely distributed trans-Andean species in Colombia, Ecuador, and Panama. However, analysis of the cytochrome b (Cytb) gene suggests the presence of cryptic diversity. Recent reviews found that morphological variation within this taxon is mainly associated with elevation. Still, mitochondrial divergence values between some populations are similar to those reported between well-diagnosable sister species in the genus. Here, we provide new Cytb sequences from Colombian and Ecuadorian specimens and morphological observations from specimens collected in different natural regions to show that C. quichua is indeed a species complex. Coendou quichua complex contains 3 separate lineages: (i) the typical C. quichua from the Andes of Ecuador; (ii) a sister lineage from the Chocó-Darién ecoregion; and (iii) an undescribed new species from wet and dry forests of the Magdalena inter-Andean valley and the Caribbean regions of Colombia. Based on morphological, ecological niche modeling, and geographical analyses, the lineage from Chocó-Darién in Colombia and Ecuador is here treated as a different species for which the name C. rothschildi is available. The lineage involving samples from the wet and dry forests of the Magdalena inter-Andean Valley and the Caribbean regions represents an unnamed taxon described herein as Coendou vossi sp. nov., endemic to Colombia.