Brotomys was described by American zoologist Gerrit Smith Miller Jr. in the early 20th century from remains found in archaeological middens of Hispaniola.

Miller also identified it with the "mohuy", an animal mentioned by the 16th-century Spanish historiographer and colonial mayor of Santo Domingo, Gonzalo Fernández de Oviedo y Valdés, in his General and Natural History of the Indies (1535): The mohuy is an animal somewhat smaller than the hutia: its color is paler and likewise gray.

This was the food most valued and esteemed by the caciques and chiefs of this island; and the character of the animal was much like the hutia except that the hair was denser and coarser (or more stiff), and very pointed and standing erect or straight above.

[5] Despite its highly sought meat, the species is thought to have been primarily driven to extinction by introduced Old World rats rather than human hunting.

[1] A mandible of Brotomys was carbon dated to 340 ± 60 years BP (1550-1670 AD), showing it survived the initial Spanish conquest of Hispaniola.