†G. thoracatus, the Little Swan Island hutia, was a third species which was found only on Little Swan Island, off northeastern Honduras. It became extinct in 1955, wiped out by storms and introduced predators. Some scientists consider it a subspecies of G. brownii.
†G. columbianus, the Cuban coney, was endemic to Cuba, where it went extinct shortly after human colonization.
†G. caymanensis, the Cayman hutia, was endemic to the Cayman Islands, where it went extinct shortly after human colonization.
Within Capromyidae, Geocapromys is the sister group to a clade comprising Mesocapromys and Mysateles on the one hand, and Capromys on the other hand. In turn, these four genera belong to the tribe Capromyini, and are the sister group to Plagiodontia.
Genus-level cladogram of the Capromyidae with their relationship to Carterodon and Euryzygomatomyinae.
^Galewski, Thomas; Mauffrey, Jean-François; Leite, Yuri L. R.; Patton, James L.; Douzery, Emmanuel J. P. (2005). "Ecomorphological diversification among South American spiny rats (Rodentia; Echimyidae): a phylogenetic and chronological approach". Molecular Phylogenetics and Evolution. 34 (3): 601–615. doi:10.1016/j.ympev.2004.11.015. PMID15683932.
^Upham, Nathan S.; Patterson, Bruce D. (2012). "Diversification and biogeography of the Neotropical caviomorph lineage Octodontoidea (Rodentia: Hystricognathi)". Molecular Phylogenetics and Evolution. 63 (2): 417–429. doi:10.1016/j.ympev.2012.01.020. PMID22327013.
^Fabre, Pierre-Henri; Galewski, Thomas; Tilak, Marie-ka; Douzery, Emmanuel J. P. (2013-03-01). "Diversification of South American spiny rats (Echimyidae): a multigene phylogenetic approach". Zoologica Scripta. 42 (2): 117–134. doi:10.1111/j.1463-6409.2012.00572.x. ISSN1463-6409. S2CID83639441.
^Upham, Nathan S.; Patterson, Bruce D. (2015). "Evolution of Caviomorph rodents: a complete phylogeny and timetree for living genera". In Vassallo, Aldo Ivan; Antenucci, Daniel (eds.). Biology of caviomorph rodents: diversity and evolution. Buenos Aires: SAREM Series A, Mammalogical Research — Sociedad Argentina para el Estudio de los Mamíferos. pp. 63–120.