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In 1606, the Spanish Empire defeated the Sultanate of Ternate, and deported the Sultan and his family to their colonial capital of Manila. The Maluku Archipelago was then incorporated into the Spanish East Indies, and was governed from the Spanish Philippine colonial capital of Manila.
The natives of the Moluccas, whether Muslim or Christian accepted Spanish rule, and decided to make a friendship with the Spanish Empire. Afterwards, the Spanish brought in many natives from the Philippines, where they helped construct churches and military garrisons in Ternate, Tidore and Ambon. They intermarried with the locals and natives of the Moluccas.
In 1663, the Chinese warlord Koxinga, who had threatened to invade Manila was killed, his army abandoning plans for the invasion. The Spanish therefore, were able to remain in the Moluccas and carry forth with their continued occupation of the islands.
Throughout the rule, the port city of Ambon was used as a stopping and checkpoint for Spanish ships in the Manila-Acapulco Galleon trade.
Its influence is still felt within the Indonesians living in the Maluku Islands, which are one of Indonesia's predominantly Christian regions. The Chavacano language, a Spanish-based creole, is spoken in the Maluku Islands.