Prehistory
The region was already inhabited by Homo erectus from approximately 1,500,000 years ago during the Middle Pleistocene age. Distinct Homo sapiens groups, ancestral to Eastern non-African (related to East Asians as well as Papuans) populations, reached the region by between 50,000BC to 70,000BC, with some arguing earlier. Rock art (parietal art) dating from 40,000 to 60,000 years ago (which is currently the world's oldest) has been discovered in the caves of Sulawesi and Borneo (Kalimantan). Homo floresiensis also lived in the area up until at least 50,000 years ago, after which they became extinct. During much of this time the present-day islands of Western Indonesia were joined into a single landmass with the Malay Peninsula known as Sundaland due to much lower sea levels. The Gulf of Thailand was dry land which connected Sundaland with Mainland Southeast Asia.
Distinctive Basal-East Eurasian (Eastern non-African) ancestry was recently found to have originated in Mainland Southeast Asia at ~50,000BC, and expanded through multiple migration waves southwards and northwards respectively, giving rise to both Oceanian (Papuan related) and basal East Asian (Onge and Tianyuan related) lineages.
Ancient remains of hunter-gatherers in Maritime Southeast Asia, such as one Holocene hunter-gatherer from South Sulawesi, had ancestry from both the Oceanian-related and East Asian-related branches of the Eastern non-African lineage. The hunter-gatherer individual had approximately ~50% "Basal-East Asian" ancestry, modeled as Onge or Tianyuan-like ancestry, and was positioned in between the Andamanese Onge and the Papuans of Oceania. The authors concluded that the presence of this ancestry in the Holocene hunter-gatherer suggests that East Asian-related admixture from Mainland Southeast Asia into Maritime Southeast Asia may have taken place long before the expansion of Austronesian societies. Geneflow of East Asian-related ancestry into Maritime Southeast Asia and Oceania could be estimated to ~25,000BC (possibly even earlier).
The pre-Neolithic Oceanian-related populations of Maritime Southeast Asia were largely replaced by the expansion of various East Asian-related populations, beginning about 50,000 to 25,000 years ago from Mainland Southeast Asia. East Asian-related ancestry was already widespread across Southeast Asia by 15,000BC, predating the expansion of Austroasiatic and Austronesian peoples.
Samples dated to c. 10,000–2000 BCE from the Hoabinhian hunter-gatherer lithic techno-complex in Mainland Southeast Asia, which predated the Austronesian and Austroasiatic expansions, display the closest genetic affinities to basal East Asian lineages related to the Upper Paleolithic Tianyuan man from northern China, as well as the prehistoric Jōmon peoples of Japan. Compared to modern populations, they share the closest affinities to the Andamanese Onge and Jarawa, and the Semang (also known as "Malaysian Negritos") and Maniq in the interior of the Malay Peninsula.
In the late Neolithic, the Austronesian peoples, who form the majority of the modern population in Brunei, Indonesia, Malaysia, the Philippines, and Timor-Leste, migrated to Southeast Asia from Taiwan in the first seaborne human migration known as the Austronesian Expansion. They arrived in the northern Philippines between 7,000 BC to 2,200 BC and rapidly spread further into the Northern Mariana Islands and Borneo by 1500 BC; Island Melanesia by 1300 BC; and to the rest of Indonesia, Malaysia, southern Vietnam, and Palau by 1000 BC. They often settled along coastal areas, replacing and assimilating the diverse preexisting peoples. The remainders of these preexisting populations, known as Negritos, form small minority groups in geographically isolated regions.
The Austronesian peoples of Southeast Asia have been seafarers for thousands of years. They spread eastwards to Micronesia and Polynesia, as well as westwards to Madagascar, becoming the ancestors of modern-day Malagasy, Micronesians, Melanesians, and Polynesians. Passage through the Indian Ocean aided the colonisation of Madagascar, as well as commerce between Western Asia, eastern coast of India and Chinese southern coast. Gold from Sumatra is thought to have reached as far west as Rome. Pliny the Elder wrote in his Natural History about Chryse and Argyre, two legendary islands rich in gold and silver, located in the Indian Ocean. Their vessels, such as the vinta, were capable to sail across the ocean. Magellan's voyage records how much more manoeuvrable their vessels were, as compared to the European ships. A slave from the Sulu Sea was believed to have been used in the Magellan expedition as a translator.
Studies presented by the Human Genome Organisation (HUGO) through genetic studies of the various peoples of Asia show empirically that there was a single migration event from Africa, whereby the early people travelled along the south coast of Asia, first entered the Malay Peninsula 50,000–90,000 years ago. The Orang Asli, in particular the Semang who show Negrito characteristics, are the direct descendants of these earliest settlers of Southeast Asia. These early people diversified and travelled slowly northwards to China, and the populations of Southeast Asia show greater genetic diversity than the younger population of China.
Solheim and others have shown evidence for a Nusantao maritime trading network ranging from Vietnam to the rest of the archipelago as early as 5000 BC to 1 AD. The Bronze Age Dong Son culture flourished in Northern Vietnam from about 1000 BC to 1 BC. Its influence spread to other parts Southeast Asia. The region entered the Iron Age era in 500 BC, when iron was forged also in northern Vietnam still under Dong Son, due to its frequent interactions with neighbouring China.
Most Southeast Asian people were originally animist, engaged in ancestors, nature, and spirits worship. These belief systems were later supplanted by Hinduism and Buddhism after the region, especially coastal areas, came under contact with Indian subcontinent during the first century. Indian Brahmins and traders brought Hinduism to the region and made contacts with local courts. Local rulers converted to Hinduism or Buddhism and adopted Indian religious traditions to reinforce their legitimacy, elevate ritual status above their fellow chief counterparts and facilitate trade with South Asian states. They periodically invited Indian Brahmins into their realms and began a gradual process of Indianisation in the region. Shaivism was the dominant religious tradition of many southern Indian Hindu kingdoms during the first century. It then spread into Southeast Asia via the Bay of Bengal, Indochina, then Malay Archipelago, leading to thousands of Shiva temples on the islands of Indonesia as well as Cambodia and Vietnam, co-evolving with Buddhism in the region. Theravada Buddhism entered the region during the third century, via maritime trade routes between the region and Sri Lanka. Buddhism later established a strong presence in Funan region in the fifth century. In present-day mainland Southeast Asia, Theravada is still the dominant branch of Buddhism, practised by the Thai, Burmese, and Cambodian Buddhists. This branch was fused with the Hindu-influenced Khmer culture. Mahayana Buddhism established presence in Maritime Southeast Asia, brought by Chinese monks during their transit in the region en route to Nalanda. It is still the dominant branch of Buddhism practised by Indonesian and Malaysian Buddhists.
The spread of these two Indian religions confined the adherents of Southeast Asian indigenous beliefs into remote inland areas. The Maluku Islands and New Guinea were never Indianised and its native people were predominantly animists until the 15th century when Islam began to spread in those areas. While in Vietnam, Buddhism never managed to develop strong institutional networks due to strong Chinese influence. In present-day Southeast Asia, Vietnam is the only country where its folk religion makes up the plurality. Recently, Vietnamese folk religion is undergoing a revival with the support of the government. Elsewhere, there are ethnic groups in Southeast Asia that resisted conversion and still retain their original animist beliefs, such as the Dayaks in Kalimantan, the Igorots in Luzon, and the Shans in eastern Myanmar.