Coendou comprises the most speciose genus in Erethizontidae, with 15 currently recognized species. Although several taxonomic studies in the last two decades have unveiled part of its diversity, the most widespread Neotropical taxon Coendou prehensilis has received limited attention. Here, we combined morphological and molecular datasets to infer the phylogenetic relationships of the species in the genus and revise the taxonomy of the C. prehensilis complex. We found four morphotypes and three well-supported monophyletic clades within C. prehensilis. These three clades represent valid species: C. prehensilis (restricted to the north of the Atlantic Forest), C. baturitensis (occurring in the eastern Amazonian and montane forests enclaves in the Caatinga), and C. longicaudatus (two subspecies, C. l. longicaudatus from the Amazon and C. l. boliviensis from Cerrado and Chaco). Furthermore, we recovered three morphologically diagnosable clades within Coendou, for which we assigned subgeneric names. Coendou (Coendou) comprises six species (C. baturitensis, C. longicaudatus, C. mexicanus, C. prehensilis, C. quichua, and C. rufescens), Coendou (Sphiggurus) includes five taxa (C. bicolor, C. insidiosus, C. nycthemera, C. speratus, and C. spinosus), and the third subgenus we named Coendou (Caaporamys) subgen. nov, comprising C. melanurus (type species), C. vestitus, C. pruinosus, C. ichillus, and C. roosmalenorum.