During the 15th and 16th centuries, the area was generally within the sphere of influence of the powerful sultanate on the island of Ternate. A larger region, called Moro, included the island of Morotai and parts of the North Halmahera coastline. The
Portuguese were a formidable presence in the area and they built a number of fortifications and controlled the island
Ternate, off the southwest coast of the North Halmahera Regency. In the mid-16th century, a Portuguese
Jesuit mission visited Halmahera and
Morotai. This created conflict with Muslims who at the time controlled Ternate and Halmahera and in 1571, they drove the
Christians from Morotai. In the early 17th century, the town of Dodinga, strategically located on Halmahera's west coast grew in influence. In 1627 and 1628,
Sultan Hamzah of
Ternate had much of the Christian population of the island moved to
Malaya, on Ternate. These developments have also increased religious tension in the region.{{cite book|url=https://books.google.com/books?id=KYXE-KJYqzQC&q=north+halmahera&pg=PA337 When the decision was made to create the regency of North Halmahera, it was promised in the
national parliament in Jakarta that a duty-free port similar to
Batam would be established on Morotai Island. However, this never happened, as internal conflict led to a demand that Morotai should be separated from the regency.
Hein Nemotemo, a Christian politician, rejected this move, given that Morotai is overwhelmingly Muslim. In August 2006, five members of the North Halmahera Regency legislature from
Golkar, including
Abdul Gafur lobbied in the national capital for the separation of Morotai as a new regency distinct from the North Halmahera Regency. This was approved by the Committee II in Jakarta and also by the provincial governor
Thaib Armaiyn. From February to April 2007, supporters of the Morotai separatist movement sealed off the government headquarters, demanding that Morotai should become separate immediately. The split was delayed and in 2008, Nemotemo's group were all that stood in the way of the split. Fearing a repeat of the 1999-2000 violence, Nemotemo backed down. During the
2009 elections in Indonesia a governor candidate for Morotai was elected and it became a new regency. ==Geography and environment==