Hominins first arrived in the Philippines during a period of lower global sea levels between 1 million years ago (1 mya) to 700,000 years ago (700 kya). Early migrations to its largest island Luzon happened in the Pleistocene and most likely began from the south in Borneo, an island once connected to mainland Asia. From there, hominins crossed narrow sea barriers and reached Luzon by passing through Palawan then Mindoro. The oldest known hominin fossils belong to the extinct Homo luzonensis, which inhabited present-day Cagayan Valley around 67 kya. The species was characterized by its short stature and relatively small brain.

The Philippines' early inhabitants were hunter-gatherers. Apart from wild pigs, deer, and bovines, they hunted a diverse range of large animals like rhinoceros, giant turtles, and elephants. The tools they manufactured were made of stone and were simple, irregularly shaped, convenient, and disposable. Dark-skinned, short-statured, and frizzy-haired peoples called Aytas or Negritos reached the archipelago by about 5040 kya and were the first anatomically modern humans to do so.

The current demarcation between this period and the early history of the Philippines is April 21, 900, which is the equivalent on the Proleptic Gregorian calendar for the date indicated on the Laguna Copperplate Inscription—the earliest known surviving written record to come from the Philippines. This period saw the immense change that took hold of the archipelago from Stone Age cultures in 50000 BC to the emergence of coastal trading centers in the fourth century, continuing on with the gradual widening of trade until 900 and the first surviving written records.

Background The Philippines is an archipelago that lies in the Earth's tropics, giving it a warm climate and making it prone to severe rainfall. Physical, chemical, and biological processes in humid environmentssuch as thermal decomposition, weathering, erosion, and bioturbationmake organic matter and sediments hard to preserve and easy to destroy. Finding samples that would otherwise be useful in constructing a detailed archaeological record is therefore difficult. For example, there is currently a scarce amount of bones discovered in archaeological sites across the country.

Pleistocene

Arrival of the first hominins

Means of traveling Early hominin species first populated the Philippines by crossing the surrounding waters during the Last Glacial Period, when sea levels were lower and present-day islands were easier to reach due to land bridges and narrower straits. These migrations began in the Chibanian (Middle Pleistocene) age, between 1 million to 700 thousand years before present (YBP).; . It was possible for hominins to reach a new island purely by accident.

There is currently no material evidence that hominins built watercraft capable of navigating the Philippine seas. Regardless, they must have found a way to drift or raft across vast expanses of water, with floating vegetation as proposed objects for doing so. Archaeologist Thomas Ingicco suggested that mangroves uprooted by disasters like typhoons could serve as such natural rafts.

Migration routes To reach the Philippines during the Pleistocene, hominins had to come from either the north in Taiwan or the south in Borneo. Borneo was the most likely starting point. It was fairly close to the Philippines and, due to low sea levels, was connected to mainland Asia through the Sundaland landmass. Hominins from Borneo would have reached Luzon by passing through Palawan first, followed by Mindoro; they may have also entered the Philippines via the Sulu Archipelago.

Sulawesi, an Indonesian island to the south, was also a likely starting point for hominin migration. Hominins coming from Sulawesi would have arrived at the Philippines via Mindanao. Although possible, the least likely migration scenario is a sea crossing from Taiwan to Luzon via the Luzon Strait. The ocean currents were highly turbulent and required advanced navigation technologies to overcome.

Early hominin activity

Hominin activity in the Philippines dates back to YBP, during the Middle Pleistocene. The earliest known evidence comes in the form of 57 stone tools discovered in Rizal, Kalinga province, alongside the remains of a butchered ancient rhinoceros. Their ages were determined using radiometric and electron spin resonance dating methods. Cut marks on 13 bones showed that flesh was removed from the animal's carcass; percussion marks on the humeri suggested they were smashed apart for extracting marrow. The discovery hints at the presence of Homo erectusor a species related to H. erectusin the area. Other megafauna fossils found in Kalinga and the rest of Luzon showed that stegodonts, elephants, giant tortoises, and giant rats were also hunted for food.

In General Tinio, Nueva Ecija province, 18 modified stone tools were found on the foothills of the Sierra Madre. The excavation site, Arubo 1, yielded several bifacial tools, such as a cleaver and a hand axe with one almost-fully modified face. The tools had unusually formal shapes, and they showed signs of organized production, careful curation, and versatility. These were atypical for most prehistoric stone artifacts in the Philippines, which were crudely made, expedient, and easily disposable. The Arubo tools were larger than those from Rizal and probably of a similar age. They were likely of Middle Pleistocene, Lower Paleolithic origin, but exact dating is unfeasible since the area had been disturbed prior to discovery.

Homo luzonensis

The oldest known hominin fossils are attributed to the extinct Homo luzonensis. The species' evolutionary origins are unclear. It might have descended from Indonesian H. erectus groups that had dispersed across island Southeast Asia (ISEA) and speciated after a period of geographic isolation. H. luzonensis probably coexisted with multiple hominin species, including H. erectus, in the Philippines.

Traditionally, H. luzonensis remains have been dated to around 67 kya. More recent studies suggest they might be as old as kya. The fossils were discovered in Callao Cave, located in the municipality of Peñablanca in Cagayan province. Included in the discovery were several unusually small teeth, suggesting that H. luzonensis was presumably diminutive and small-brained, although making accurate estimates about their height and size is hard due to a lack of fossils. The remains were found alongside several deer, pig, and bovine bones, some of which had cut marks that suggested animal butchery.

Presence of anatomically modern humans

Anatomically modern humans (Homo sapiens) are estimated to have colonized the Philippines and the rest of ISEA by 5040 kya, in the Tarantian or Late Pleistocene. Their subsistence strategies are characterized by a hunter-gatherer lifestyle, high mobility, complex fishing and seafaring technologies, crude and expedient tools, and early ritual practices. The first modern humans to reach the archipelago are commonly referred to as Aytas or Negritos. They had dark skin, short stature, frizzy hair, and high levels of ancestry from Denisovans, archaic hominins that had interbred with H. sapiens upon their arrival in Southeast Asia.

Between 3533 kya, modern humans had already reached Mindoro, arriving from the southwest through Palawan. The given date is based on AMS radiocarbon dating techniques performed on artifacts from three sites in southern Mindoro. H. sapiens inhabiting the islands did not have advanced stone technologiestheir simple tools were presumably made from shells and beach pebbles. They had a wide variety of food options, like fish, molluscs, macaques, rats, porcupines, pangolins, wild pigs, tamaraws, deer, reptiles, and tigers. Pilanduk Cave in Palawan and Bilat Cave in Mindoro are currently the only sites that contain evidence for human activity during the Last Glacial Maximum (2520 kya), when sea levels were at their lowest.

Fossilized fragments of a skull and jawbone of three individuals had been discovered on May 28, 1962 by Dr. Robert B. Fox, an American anthropologist of the National Museum.; , citing . These fragments are collectively called "Tabon Man" after the place where they were found on the west coast of Palawan. Tabon Cave appears to be a kind of a Stone Age factory, with both finished stone flake tools and waste core flakes having been found at four separate levels in the main chamber. Charcoal left from three assemblages of cooking fires there has been Carbon-14 dated to roughly 7,000, 20,000, and 22,000 BC.. These remains are the oldest modern human remains found on the islands, and have been U/Th-dated to 47,000 ± 11–10,000 years ago. (In Mindanao, the existence and importance of these prehistoric tools was noted by famed José Rizal himself, because of his acquaintance with Spanish and German scientific archaeologists in the 1880s, while in Europe.)

Tabon Cave is named after the "Tabon bird" (Tabon scrubfowl, Megapodius cumingii), which deposited thick hard layers of guano during the period when the cave was still uninhabited, resulting to a cement-like floor made of bird dung where three succeeding groups of tool-makers settled. It is indicated that about half of the 3,000 specimens recovered from the cave are discarded cores of a material which had to be transported from some distance. The Tabon man fossils are considered to have come from the third group of inhabitants who inhabited the cave between 22,000 and 20,000 BC. An earlier cave level lies so far below the level containing cooking fire assemblages that it must represent Upper Pleistocene dates from 45 or 50 thousand years ago.

Physical anthropologists who have examined the Tabon Man skullcap have agreed that it belonged to a modern man (Homo sapiens), as distinguished from the mid-Pleistocene Homo erectus species. This indicates that Tabon Man was Pre-Mongoloid (Mongoloid being the term anthropologists apply to the racial stock which entered Southeast Asia during the Holocene and absorbed earlier peoples to produce the modern Malay, Indonesian, Filipino, and "Pacific" peoples). Two experts have given the opinion that the mandible is "Australian" in physical type, and that the skullcap measurements are most nearly like the Ainus or Tasmanians. Nothing can be concluded about Tabon man's physical appearance from the recovered skull fragments except that he was not a Negrito.

The custom of Jar Burial, which ranges from Sri Lanka, to the Plain of Jars, in Laos, to Japan, also was practiced in the Tabon caves. A spectacular example of a secondary burial jar is owned by the National Museum, a National Treasure, with a jar lid topped with two figures, one the deceased, arms crossed, hands touching the shoulders, the other a steersman, both seated in a proa, with only the mast missing from the piece. Secondary burial was practiced across all the islands of the Philippines during this period, with the bones reburied, some in the burial jars. Seventy-eight earthenware vessels were recovered from the Manunggul cave, Palawan, specifically for burial.

Human remains in the cave are from both large and small individuals. The latter fit well with Philippine negritos who were among the archipelago's earliest inhabitants, descendants of the first human migrations out of Africa via the coastal route along southern Asia to the now sunken landmasses of Sundaland and Sahul.

Holocene