[1][2] The etymology of the genus name derives from the two ancient greek words φύλλον (phúllon), meaning "plant leaf", and μῦς (mûs), meaning "mouse, rat".

[3][4] Phyllomys is the sister genus to Echimys, and then to Makalata.

These taxa are closely related to the genera Pattonomys and Toromys.

In turn, these five genera share phylogenetic affinities with a clade containing the bamboo rats Dactylomys, Olallamys, Kannabateomys together with Diplomys and Santamartamys.

[5] Isothrix Lonchothrix   (Tuft-tailed spiny tree-rat) Mesomys Pattonomys Toromys   (Giant tree-rat) Makalata Echimys Phyllomys Diplomys Santamartamys   (Red-crested tree-rat) Kannabateomys   (Atlantic bamboo rat) Dactylomys Olallamys There are thirteen named species in the genus.