[1] The term Clyomys derives from the two ancient greek words κλύω (klúō, or clyo), meaning "to listen, to prick up one's ears", and μῦς (mûs), meaning "mouse, rat".

In turn, these three genera — forming the clade of Euryzygomatomyinae — share phylogenetic affinities with a clade containing Carterodon and members of the family Capromyidae.

[5] Analyses of craniodental characters proposed that Clyomys — and also Euryzygomatomys — may be associated with Carterodon.

[6][7] However, molecular data suggest the polyphyly of this assemblage of fossorial genera.

[5] Trinomys (Atlantic spiny rats) Clyomys Euryzygomatomys (guiaras) Carterodon (Owl's spiny rat) Plagiodontia Geocapromys Capromys (Desmarest's hutia) Mesocapromys Mysateles