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Ambon was colonized by Portugal in 1526, until the Portuguese were driven out by the Dutch in 1609. Except for brief periods of British rule, the island remained under Dutch control until Indonesia's independence in 1948. During the Dutch period, Ambon City was the seat of the Dutch resident and military commander of the Moluccas. The town was protected by Fort Victoria, and a 1911 encyclopedia characterized it as "a clean little town with wide streets, well planted". The population was divided into two classes: orang burger or citizens, and orang negri or villagers, the former being a class of native origin enjoying certain privileges conferred on their ancestors by the old Dutch East India Company. There were also, besides the Dutch, some Arabs, Chinese and a few Portuguese settlers. Ambon City was the site of a major Dutch naval base, which was captured in World War Two by the Japanese in 1942. Ambon was a center of Christian missionary activity, and Ambon and the surrounding islands have many Christians as well as the Muslims that predominate in most of Indonesia.
In 1950, Ambon City was the center of an uprising against Indonesian rule, which resulted in the Republic of the South Moluccas declaring its independence from Indonesia. Indonesia reasserted control in 1952. Nationalist sentiment continued on the islands, as well as tensions between Christians and Muslims. Intercommunal violence between Christians and Muslims broke out in 2000, and resulted in the destruction of parts of Ambon City, including parts of Pattimura University. Fighting has erupted sporadically since 2000, and many Ambonese have been displaced by the violence.
Nowadays, the city is peaceful and security is under control. The harmful element Laskar Jihad has disbanded itself in October 2002, while the military and police has continuously received surrendered arms and weapons.
The city of Ambon is still partially segregated along religious lines, due to painful memories from the conflict. However, since the peace accord, people from both faiths has had increasing rate of interaction through trade and commerce, and multifaith schools are appearing once more. Reconciliation and full desegregation is still some way off, but Ambon is heading towards the right way.