The Portuguese were aware of the islands early in the 17th century: a map dated 1606 shows Siberut as "Mintaon". In August 1792 John Crisp, an employee of the British East India Company, visited the Pagai ("Poggy") islands at his own expense to study the Mentawai people. His account was published in 1799, providing the first details of the Mentawai people in western literature. The Mentawai Islands officially became part of the Dutch East Indies on 10 July 1864, not having been subject to the Anglo-Dutch Treaty of 1824. In 1901 the German Royal Missionary Society established a presence on the south coast of North Pagai island at the invitation of the Dutch colonial authorities. The first missionary was murdered, and it wasn't until 1915 that the first person was converted, with the program then being extended to other islands.
After Indonesian independence, Catholic Italian missionaries established a presence in the islands. Post-independence government policies relocated the indigenous population into villages, in contrast to their traditional dispersed house groups (uma), with the aim of promoting "development". Cultural tourism started to develop in the late 1980s, and when in the mid-1990s world-class waves were discovered by some Australian surfers, surfing tourism started to develop.
The island of Siberut was extensively logged from the 1970s after the government granted logging permits for most of the island. In 1993, the logging concessions were revoked and about half the island was declared a national park. In 2001 logging recommenced after a new logging permit was granted for an area of 500 km².
The islands have been separated from Sumatra since the mid-Pleistocene period, which has allowed at least twenty endemic species to develop amongst its flora and fauna. This includes four endemic primates: the Mentawai or Kloss Gibbon (Hylobates klossii), Mentawai Macaque (Macaca pagensis), Mentawai leaf-monkey (Presbytis potenziani), and snub-nosed monkey (Simias concolor). Some areas of the Mentawai Islands rain forest ecoregion are protected, such as the Siberut National Park.
The Mentawai Islands lie on an active and powerful megathrust earthquake zone lining the south side of Sumatra island, dividing the Pacific Plate and Indian Ocean plates. Earthquake and tsunami activity has been high since the 2004 Indian Ocean earthquake. In 1833, the region was hit with an earthquake possibly similar in size to the 2004 Indian Ocean Earthquake and also another large one in 1797.