The Old Johor Fort or Kota Johor Lama was the site of fierce wars amongst the local Malays and outside invading forces. It was built in 1540 during the reign of Sultan Alauddin Riayat Shah II (1528-1564). This fort was the best defence fort built along the Johor River at the time.

After the fall of the Malay Sultanate of Melaka in 1511, it became the administrative centre and defence fort to counter-attack the Portuguese position in Melaka. The natural environment of the fort made it easier to supervise the movement of the ships especially the threat from the Acehnese and Portuguese.

In 1587, the fort fell to the Portuguese. It was burnt down and all its assets, including its cache of weapons were confiscated. The fort is surrounded by earthen walls, some 10 to 25 feet high; and two tombs can be found near the fort, are believed to be that of Sultan Alauddin and his warriors.