The Philippine burial sites of Catanauan, Quezon Province and Ille Cave & Rockshelter, El Nido, Palawan provide an interesting venue for exploring population and cultural continuity. Oftentimes, these inquiries surface when archaeological sites overlap with living spaces of present-day communities. However, oral history around these two sites indicate that contemporary communities are migrant populations. It is often surmised that the original indigenous communities that formerly resided in the area are perhaps the actual descendants of these archaeological burials. In this study, we use 3D Geometric Morphometrics to compare the cranial shape of contemporary “indigenous” populations and individuals from archaeological contexts to investigate if there are morphological affinities between these groups that may help us understand notions of population continuity in the area and potentially support ideas raised by oral accounts.