The insular radiation of hutias is remarkable among mammals for its high rate of extinction during the Holocene (∼58% of species), yet fragments of intact habitat throughout the West Indies retain a critical portion of endemic diversity needing assessment. Cuba contains 8 of the 11 recognized living species of hutias, with surviving forms also on Hispaniola, Jamaica, and the Bahamas. Herein, we performed molecular phylogenetic analyses across populations of Cuban hutias in the genera Capromys, Mesocapromys, and Mysateles to address major gaps in our understanding of their species limits, phylogenetic structure, and geographic distributions. Comparing sequences of mitochondrial genes (cyt-b, COI, 12S rRNA) from 41 individuals and 21 sites across the archipelago, we found evidence that Capromys pilorides contains a major species-level subdivision from western to eastern Cuba, spanning a greater geographic region than previously hypothesized. Populations of Capromys in each clade last shared a common ancestor ∼1.1 million years ago (Ma; 5.2% cyt-b divergence). The western clade is further subdivided between mainland hutias (C. p. pilorides) and those on Isla de la Juventud plus Cayo Cantiles (C. p. relictus has priority). The eastern clade contains all Capromys east of Sierra del Escambray in central Cuba, including mainland and insular forms. However, without paired analyses of morphology and genetics or data from type localities, we cannot assign a name to the eastern Capromys sp. nov. at this time. Divergencetime analyses across 9 named species of hutias (plus 1 extinct), including nuclear genes (GHR, vWF, RAG1), dates the Capromyidae split from their South American relatives (Echimyidae) at 15.5 Ma. The crown radiation of hutias was 8.8 Ma, with successive divergences at 5.4 Ma (Geocapromys), 3.1 Ma (Capromys), and 2.2 Ma (Mysateles–Mesocapromys). Detailed surveys are needed to assess the conservation status of these evolutionarily distinct Cuban taxa.