The recently discovered human remains from Callao Cave, northern Luzon, Philippines securely date the migration of hominins into the Philippines to ca. 70 kya (thousands of years ago). The direct route to reach Luzon from the Asian mainland is via Borneo, Palawan, through Mindoro and into Luzon. Our research focuses on Mindoro Island as a potential stepping stone to the main Philippine Archipelago. While Palawan and Luzon have produced evidence for early human occupation, no systematic research on the prehistory of Mindoro has been conducted until now. We report on recent archaeological investigations at the Bubog rockshelter sites on the small island of Ilin just off the coast of Mindoro. The excavations produced evidence of stratified sequences of human habitation at the two rockshelter sites in the form of dense shell middens that date to ca. 11 kya onwards. They provide direct evidence on how variability in landscape formation, sea levels, and landmass during the terminal Pleistocene and early Holocene influenced the behavior of early human populations. Numerous species of molluscs were recorded and provisional results indicate variations in the invertebrate faunas throughout the stratigraphic sequences, resulting from sea level rise and the establishment of coral reefs between Ilin and Mindoro at the end of the Pleistocene. Our results contribute substantially to our understanding of the processes of human island adaptation, complement ongoing research into Island Southeast Asia's paleogeography, and enhance current knowledge of prehistoric subsistence strategies across the region. © 2014 Trustees of Boston University.