Within Capromyidae, the closest relative of Mesocapromys is the genus Mysateles. Both genera are the sister group to Capromys, and then Geocapromys is a more distant genus. 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.
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