The Ilin cloud rat Crateromys paulus, identified from a single individual in 1981 and collected from an undocumented location in Ilin Island, Mindoro, Philippines, is now considered to be “data deficient” and possibly extinct. 96 murid dental fossil remains were recently recovered within a two-meter excavation of well stratified and chronometrically dated deposits at the archaeological sites of Bubog I and Bubog II on Ilin Island. Research on these well-preserved murid rodent remains confirms the past presence of C. paulus on Ilin Island and describes for the first time variability in dental morphology of this species. The succession of fossils within the detailed stratigraphic sequence also provides us with information on C. paulus throughout the Holocene and on its possible recent extinction.