Due to their intermingling within other peoples, the original genetic identity of the Sakizaya is uncertain. According to one study, they are intimately related to the Northern and Middle Amis. They also seem to share certain genetic traits with other indigenous groups, as well as with the Taiwanese Han, though this may have been a result of intermarriage. The C2 and C3 haplogroups are absent in their population.
Much of the history of the Sakizaya is unknown. It is unclear when the Sakizaya, or their ancestors, first arrived in Taiwan. According to some experts, the first human inhabitants of the island arrived 15,000 years ago and were dependent on marine life for survival. Neolithic peoples began arriving 6,000 years ago, which allowed the advent of agriculture, domestic animals, polished stone adzes, and pottery. The presence of these adzes imply a relation with the Penghu islands, where these objects are common.
The first contact with the community outside of Formosa occurred during the 17th century, when the Dutch and the Spanish arrived. It was during this time when a 1636 Spanish document was written about the name and activities of the people. Since then, there were not any reports of external contact until the 19th century.
In 1878, the Sakizaya, and their Kavalan allies, fought a devastating battle against Qing invaders. This event ended in disaster for both communities causing many of their members to be slaughtered in an event called the "Takobowan Incident" (also known as the “Galeewan Incident” or “Kalyawan Battle” zh:加禮宛事件). Others were displaced by Han settlers. The remaining Sakizaya, meanwhile, were forced to blend with other peoples, such as the Ami, with the intention of protecting their identity.
When the Japanese ruled Taiwan in 1895, anthropologists classified the people as a subgroup of the Amis. The people, however, discreetly maintained their own culture and language which continued during the next century.
In 2004, the community presented a petition for official ethnic group status to the Council of Indigenous Peoples based on historical, linguistic and cultural data. This was officially filed on 13 October 2005. Eventually, the petition was approved on 17 January 2007, recognizing them as a distinct ethnic group.
Like other Taiwanese Aborigines, the Sakizaya face contemporary social and economic challenges. These include urbanization of the youth, a phenomenon that may affect their culture.