Excavations in Callao Cave, in the lowland (ca. 85 m elevation) Cagayan River Valley of northeastern Luzon, Philippines, have produced the first fossils of any endemic genera of Philippine murid rodents. Three dentaries dated to the Late Pleistocene, between ca. 50,000 and 68,000 BP, are referred to the genera Batomys and Apomys; the former is a member of the endemic “Phloeomys Division” of Philippine murids, and the latter of the “Chrotomys Division,” also endemic to the Philippines. Batomys is currently known from five extant species from Luzon, Mindanao, and Dinagat islands; the two species known from Luzon differ in size and dental and mandibular morphology from the two fossil mandibles, and both occur only at elevations above 1350 m. Apomys is currently known from two subgenera on Luzon; the fossil is a member of the nominate subgenus, which contains two species on Luzon, one of which, Apomys microdon, is conspecific with one fossil. We hypothesize that the Batomys fossils represent a different species from the living taxa, but we do not name it due to the fragmentary nature of the specimens. These Apomys and Batomys represent the first fossil small mammals from the main body of the Philippine archipelago (east of Huxley's Line), and the Batomys are the first suspected extinct Pleistocene small mammal from the Philippines. The fossils indicate greater species richness and broader distributions than at present within this distinctive and diverse endemic radiation of mammals.