The city is near the site of the former capital of the Johor Sultanate, Kota Batu, which was established by Alauddin Riayat Shah II shortly after the fall of the Sultanate of Malacca in 1511. Kota Batu was sacked and burnt by the Acehnese in 1564, and Alauddin was taken to Aceh and killed. The capital was then moved to Bukit Seluyut for a few years.
In the early 1570s, the sultan Ali Jalla reestablished the capital at Johor Lama. The Johor Sultanate had initially formed an alliance with the Portuguese against the Acehnese, however Ali Jalla confiscated the cargo of a Portuguese ship that had wrecked on the mouth of the Johor River. In response, the Portuguese stopped traders from Melaka from trading with Johor. Ali Jalla then forced ships to go Johor Lama, and attacked Melaka in January 1587. In retaliation, the Portuguese blockaded the Johor River, then launched an attack on Johor Lama later in the year. The fortified city was defended by 12,000 men, but the Portuguese prevailed and destroyed the fort. The capital of Johor was then moved to Batu Sawar further up the Johor River.
Concerning the destruction of Johor Lama by the Portuguese in 1587:
- Borschberg, Peter, The Singapore and Melaka Straits. Violence, Security and Diplomacy in the 17th Century, NUS Press, 2010. https://www.academia.edu/4302722
- Borschberg, Peter, Singapore and the Destruction of Johor Lama in 1587, Singapore, 2015. https://www.academia.edu/12955566
- Borschberg, Peter, The Memoirs and Memorials of Jacques de Coutre, Singapore: NUS Press, 2014. https://www.academia.edu/4302708
- Pinto, Paulo J. de Sousa, The Portuguese and the Straits of Melaka, 1575–1619. Power, Trade and Diplomacy, Kuala Lumpur and Singapore: MBRAS and NUS Press, 2012.
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