The French Polynesian island groups do not share a common history before the establishment of the French protectorate in 1889. The first French Polynesian islands to be settled by Polynesians were the Marquesas Islands in AD 300 and the Society Islands in AD 800.

European discovery began in 1521 when the Portuguese explorer Ferdinand Magellan sighted Pukapuka in the Tuamotu Archipelago. Dutchman Jakob Roggeveen discovered Bora Bora in the Society Islands in 1722, and the British explorer Samuel Wallis visited Tahiti in 1767. The French explorer Louis Antoine de Bougainville visited Tahiti in 1768, while the British explorer James Cook visited in 1769. Christian missions began with Spanish priests who stayed in Tahiti for a year from 1774; Protestants from the London Missionary Society settled permanently in Polynesia in 1797.

King Pomare II of Tahiti was forced to flee to Moorea in 1803; he and his subjects were converted to Protestantism in 1812. French Catholic missionaries arrived on Tahiti in 1834; their expulsion in 1836 caused France to send a gunboat in 1838. In 1842, Tahiti and Tahuata were declared a French protectorate, to allow Catholic missionaries to work undisturbed. The capital of Papeete was founded in 1843. In 1880, France annexed Tahiti, changing the status from that of a protectorate to that of a colony.