Human fossil records indicate that the Philippines may have been inhabited for thousands of years. According to earlier archaeological findings, the first man in the Philippines came from the islands around Asia which Professor H. Otley Beyer, eminent American authority on Philippine archeology and anthropology, dubbed the "Dawn Man". Yet the oldest human fossil found in the Philippines thus far is the 22,000-year-kull cap of a "Stone-Age Filipino" discovered by Dr. Robert B. Fox, an American anthropologist of the National Museum, inside Lucy Cave, Palawan, on May 28, 1962 and dubbed the "Tabon Man". The Tabon caves of Palawan indicate settlement for at least 30,500 years; these hunter-gatherers used stone flake tools. After these early settlers, the Negrito arrived, whose ancestors include the Ati and the Aeta.
 
An Ati woman in Boracay, whose tribe belong to the Negritos, the earliest surviving inhabitants of the PhilippinesThe Austronesian-speaking peoples originated from Proto-Austronesian peoples in South China, coastal Southeast Asia, and island Southeast Asia. The two best known hypotheses are that the Austronesian languages developed either in Taiwan about 7,000 years ago or in island Southeast Asia. The Malayo-Polynesian-speaking peoples, an Austronesian branch, settled in the Philippines about 3,000 BC, and spread eastward to the Pacific Islands, and westward to Madagascar.

The Philippines had trade relations with China and Japan and strong cultural ties with India through neighboring present-day Malaysia and Indonesia as early as the 9th to the 12th century. The social and political organization of the population, in the widely scattered islands, evolved into a generally common pattern. Only the permanent-field rice farmers of northern Luzon had any concept of territoriality. The basic unit of settlement was the barangay, originally a kinship group headed by a datu (chief). Within the barangay, the broad social divisions consisted of the maharlika (nobles), including the datu; timawa (freemen); and a group described before the Spanish period as dependents. Dependents included several categories with differing status: landless agricultural workers; those who had lost freeman status because of indebtedness or punishment for crime; and alipin (slaves), most of whom appear to have been war captives.

Islam was brought to the Philippines by traders and proselytizers from Malaysia and Indonesia. Islamization of the Philippines is due to the strength of Muslim India. By the 13th century, Islam was established in the Sulu Archipelago and spread from there to Mindanao; it had reached the Manila area by 1565. Although Islam spread to Luzon, Animism, syncretized with Hinduism and Vajrayana Buddhism, was still the religion of the majority of the Philippine islands. Muslim immigrants introduced a political concept of territorial states ruled by rajas or sultans who exercised suzerainty over the datu. Neither the political state concept of the Muslim rulers nor the limited territorial concept of the sedentary rice farmers of Luzon, however, spread beyond the areas where they originated. When the Spanish arrived in the 16th century, the majority of the estimated 500,000 people in the islands lived in barangay settlements.

Timeline of Philippine History

Spanish Rule (1565-1898)