When the Portuguese appeared in Maluku from 1512, Bacan was a significant local realm with more men and ships than Ternate, Tidore or Jailolo. Linguistic research has shown that
Bacan Malay is closer to
Melaka Straits Malay than other Malay dialects in Maluku, pointing at early strong relations with traders from the
Malay World. The royal seat was not on Bacan Island as it was in later times but rather on Kasiruta. The power of the sultan extended to Ceram which was economically vital due to trade in forest products, largely coming from the Papuan lands. Clove production was small compared to the other Malukan islands, though it grew rapidly up to the mid 16th century.
Tomé Pires (c. 1515) says that the name of the ruler was Raja Yusuf, who was the half-brother of
Bayan Sirrullah of Ternate. In 1521 the remnants of the
Magellan expedition arrived to Tidore where the
Spanish seafarers were approached by the sultans of Tidore, Jalolo and Bacan as potential allies against the
Portuguese intruders. The ruler of Bacan at the time was married to a daughter of the pro-Portuguese Bayan Sirrullah, but had a fallout with his father-in-law who was promptly poisoned by the couple. The Bacanese moreover massacred a party of Portuguese who carelessly abused the wives of the locals and even the court ladies. (large outrigger geared for warfare) in a manuscript from 1561 During the next decades Bacan played a subordinate role in relation to Ternate and Tidore. A sultan called Alauddin (I) appears in the 1520s and lived in a shifting state of alliance and hostility with the Portuguese. When he tried to keep aloof of the Europeans, a Portuguese expedition raided the capital in 1534 and even destroyed the royal graves. By the mid 16th century the sultanate produced as much cloves as Ternate. It was an important port of call for ships going from Ternate to other parts of the archipelago, and from
Banda or
Ambon to Ternate. Papuan chiefs sometimes visited Bacan with their vessels and had friendly ties with the sultan. Alauddin's son and successor was Hairun (1557-1577), not to be confused with his maternal uncle
Hairun of Ternate. Islam was still confined to a thin layer of society while most inhabitants followed local religious practices. Hairun was on bad terms with his similarly-named uncle of Ternate. He therefore sought support with the Portuguese and converted to Catholicism, adopting the name Dom João. The conversion of the ruler and part of the inhabitants led to trouble after 1570. The new Ternatan ruler
Babullah, a cousin and brother-in-law of Dom João, held a strongly Muslim and anti-Portuguese position and attacked Christianized areas of Maluku, including Bacan. While the Portuguese were expelled from Ternate in 1575, Dom João was forced to revert to Islam; nevertheless, Babullah sent emissaries who poisoned his cousin in 1577. Bacan was badly ravaged in the process and its history in the next decades is rather obscure. A son or brother of Dom João, Dom Henrique, was allowed by Ternate to fill the throne but soon started to collude with the Portuguese and was killed in battle in 1581. Christianity was largely suppressed, though a congregation remained in
Labuha on Bacan Island under troubled conditions. Of Bacanese royalty there remained a young son of Dom João called Alauddin II (1581-c. 1609) who, although a Muslim, strove to cast off the Ternatan yoke. The death of the powerful Babullah (1583) and the
Spanish-Portuguese union (1581) made for opportunities, as the Spanish tried to master Maluku from their bases in the
Philippines. Alauddin II assisted an Iberian invasion in 1603 where he was personally wounded, and again in 1606. On the last occasion the Spanish were entirely successful in defeating the Ternate Sultanate and rewarded Alauddin II with the islands of
Kayoa, Waidoba and Bayloro. However, the long series of conflicts had taken a heavy toll: the population of the sultanate had declined and the sultan only played a marginal role in the affairs in Maluku. The old residence in Kasiruta had been abandoned by the early 17th century and the palace was moved to
Amassing on the south-west side of Bacan Island, close to Labuha. According to the Bacan Chronicle, Alauddin gave his daughter in marriage to Patra Samargalila, the Sangaji (chief) of Labuha. The Sangaji and his wife then persuaded Alauddin to move his seat to the vicinity of Labuha since it was a good land with a fine river. Dutch sources indicate that fear of the lethal raids carried out by Tidorese war fleets was decisive in the move. ==Dutch overlordship==