The large Mindoro forest mouse belongs to the "Chrotomys" division, a group within the Murinae that occurs exclusively on the Philippines and in addition to "Apomys" also includes "Rhynchomys", "Chrotomys" and "Archboldomys". Animals in this division share several morphological and genetic features. Within this group, "Apomys" is by far the biggest and most extensive genus, containing small, inconspicuous wood mice which are common to the whole of the Philippines, while the other, more specialized genera are barely ever found outside Luzon. "Apomys" itself was divided in two groups by American biologist Guy Musser in 1982, the first being the "datae" group, containing only the Luzon montane forest mouse ("A. datae"), and the second the "abrae-hylocetes" group, containing all other species. Animals in these two groups differ in the way in which the head is supplied with blood from arteries. Ruedas placed the large Mindiro forest mouse in the "datae" group. This relationship is further supported by other similarities: both species are relatively large for the genus and have a relatively long snout.