Lying within Wallacea (mostly east of the biogeographical Weber Line), the Moluccas have been considered a geographical and cultural intersection of Asia and Oceania.

A second influx of immigrants primarily from Java began in the early 20th century under the Dutch and continues in the Indonesian era, which has also caused a lot of controversy as the Transmigrant programs are thought to be a contributing factor to the Maluku Riots.

Another possibility is that the word originates from the word maloko, which is a combination of the particle ma- and the root loko in North Halmahera languages means the variety of words relating to the location of mountains, in which case "Maloko Kie Raha" in the phrase "Ternate se Tidore, Moti se Mara Maloko Kie Raha" means "Ternate, Tidore, Moti, and Mara the place of the four mountains" or with the shifting of pronunciation of loko towards luku, means "Ternate, Tidore, Moti, and Mara the world of the four mountains".

[11] Other archaeological finds showed possible[clarification needed] Arab merchants began to arrive in the fourteenth century, bringing Islam.

A story from Letvuan on the island of Kai Kecil tells of a Balinese envoy of Gajah Mada by the name of Kasdev, his wife Dit Ratngil, and eight of their children.

Archaeological sites of ancient tombs found in Sorbay Bay, south of Letvuan, seem to support the story, as well as some cultural practices of Kei of Balinese origin.

An oral story reports of a 14th-century Majapahit expedition to Negeri Ema, Ambon Island, by an envoy named Nyi Mas Kenang Eko Sutarmi alongside 22 people among her retinue and a spear-bearer trying to form an alliance and trading relationship with Negeri Ema's leader by the name of Kapitan Ading Adang Anaan Tanahatuila.

Archaeological finds relating to this expedition include a water source with Sun symbols with nine rays, and heirlooms of spears and Totobuang kept by the Maitimu family and village office of Negeri Ema, alongside many potteries.

The most significant lasting effects of the Portuguese presence were the disruption and reorganization of the Southeast Asian trade, and in eastern Indonesia—including Maluku—the introduction of Christianity.

The rulers of the competing island states of Ternate and Tidore also sought Portuguese assistance and the newcomers were welcomed in the area as buyers of supplies and spices during a lull in the regional trade due to the temporary disruption of Javanese and Malay sailings to the area following the 1511 conflict in Malacca.

[18] Allying himself with Ternate's ruler, Serrão constructed a fortress on that tiny island and served as the head of a mercenary band of Portuguese seamen under the service of one of the two local feuding sultans who controlled most of the spice trade.

[19] Following Portuguese missionary work, there have been large Christian communities in eastern Indonesia through to contemporary times, which has contributed to a sense of shared interest with Europeans, particularly among the Ambonese.

[20] The Dutch East India Company in the course of Dutch–Portuguese War allied with the Sultan of Ternate and conquered Ambon and Tidore in 1605, expelling the Portuguese.

This included the genocidal conquest of the nutmeg-producing Banda Islands in 1621, the elimination of the English in Ambon in 1623, and the subordination of Ternate and Tidore in the 1650s.

An anticolonial resistance movement led by a Tidore prince, the Nuku Rebellion, engulfed large parts of Maluku and Papua in 1780-1810 and co-opted the British.

[21] With the declaration of a single republic of Indonesia in 1950 to replace the federal state, a Republic of South Maluku (Republik Maluku Selatan, RMS) was declared and attempted to secede,[citation needed] led by Chris Soumokil (former Supreme Prosecutor of the Eastern Indonesia state) and supported by the Moluccan members of the Netherlands KNIL special troops.

The subsequent 18 months were characterized by fighting between local groups of Muslims and Christians against jihadist groups from Java and the Indonesian military backing them leading to the destruction of thousands of houses, the displacement of approximately 500,000 people, the loss of thousands of lives, and the segregation of Muslims and Christians.

[24] The geology of the Maluku Islands shares much similar history, characteristics, and processes with the neighbouring Nusa Tenggara region.

Flora and fauna immigration between islands is thus restricted, leading to a high rate of endemic biota evolving.

Maluku is the subject of two major historical works of natural history by Georg Eberhard Rumphius: the Herbarium Amboinense and the Amboinsche Rariteitkamer.

[27] Rainforest covered most of northern and central Maluku, which, on the smaller islands has been replaced by plantations, including the region's endemic cloves and nutmeg.

[24] Bird species include approximately 100 endemics with the greatest variety on the large islands of Halmahera and Seram.

[24] Over 130 languages were once spoken across the islands; however, many have now switched to the creoles of Ternate and Ambonese, the lingua franca of northern and southern Maluku, respectively.