The New World porcupines of the genus Coendou comprise 16 species of arboreal nocturnal rodents. Some of these species are poorly known and have not been included in phylogenetic analyses. Based on recently collected specimens with associated tissue from the Brazilian Amazonia, we investigate the distribution and phylogenetic relationships of Roosmalens’ dwarf porcupine, Coendou roosmalenorum, using an integrative approach using mitochondrial gene sequences and morphological data from new specimens and localities. Our results recovered C. roosmalenorum in the subgenus Caaporamys. However, analyses of our molecular and combined datasets produced different topologies. The new record shows the presence of C. roosmalenorum 480 km to the southeast of the Rio Madeira and 95 km away from Rio Juruena in Mato Grosso state, indicating a wider distribution in southern Amazonia than suspected. All known records of C. roosmalenorum are in the Madeira biogeographical province, to which it might be endemic.