It has an area of some 2,336.6 km2 (902.2 sq mi), including Rao Island which lies to the west of Morotai and forms an administrative district within the regency.

During the fifteenth and sixteenth centuries, Morotai was generally within the sphere of influence of the powerful sultanate on the island of Ternate.

It was the core of a larger region, called Moro, that included the island and the coastline of Halmahera closest to Morotai to the south.

The Muslim states on Ternate and Halmahera resented the outpost for its evangelising activities, and managed to drive the mission from the island in 1571, as a part of a larger Portuguese retreat in the region.

In the seventeenth century, Ternate further exerted its power over Morotai by repeatedly forcing major parts of the population to move off the island.

Early in the century most of the population was moved to Dodinga, a small town in a strategic spot on Halmahera's west coast.

[6] Two thirds of them were engineers, who rapidly established facilities including harbours and two airstrips[6] plus extensive fuel stores.

The last confirmed Japanese holdout from the war, Private Teruo Nakamura (Amis: Attun Palalin), was discovered by the Indonesian Air Force on Morotai, and surrendered to a search patrol on December 18, 1974.

[10] Within hours, a Douglas C-47 Skytrain transport aircraft landed on the now captured airstrip, carrying senior Permesta representative and two Americans.

[12] Thereafter the rebellion was largely confined to the Minahasa Peninsula of Sulawesi, where Permesta remnants waged a guerilla campaign until the last unit surrendered in January 1962.

It has an area of some 2,336.6 square kilometres (902.2 sq mi), including Rao Island off the west coast of Morotai.

Note: (a) the population in 2010 of Rao Island is included in the figure for Morotai Selatan Barat District, from which it was cut out.