Modern anthropologists dislike talking about physical distinctions; however from the 16th century Spanish missionaries on, European invaders have spoken of people with three sets of distinct physical characteristics:

This has provided much of the stimulus for the elaboration of various "migration wave" theories, inspired by the tracing of cultural influences from Southeast Asia, India, the Middle East, and China. One of the most elaborate of these was developed by anthropologist H.O. Beyer in the early 20th century, and involved eight waves of prehistoric H. Sapiens immigrants:

It should be remarked that the various "waves of migration" theories are still largely unsubstantiated and highly controversial. Most modern anthropologists see Beyer's scheme as rather overblown; nevertheless it is evident that the Philippines have seen many episodes of large-scale immigration.

"Negrito"
"Indonesian"
"Malayan"
Physical Characteristics