Johor Lama is famous for its historical sites, reflecting the continuity of the Malacca Malay Sultanate to the Johor Malay Sultanate. In fact, since the defeat of Malacca at the hands of the Portuguese in 1511, it was Johor that took over the role previously played by Malacca. The Johor Sultanate was also the only government in the Malay Archipelago that was capable of resisting the Portuguese. In addition, Sultan Alauddin who became the first Sultan of Johor was the son of Sultan Mahmud, the last Sultan of Malacca. Therefore, the task of fighting the Portuguese colonists had become the responsibility of the Johor rulers from thenceforth.
Johor Lama that was made the administrative centre of the Johor Sultanate has important historical sites to be valued. Among them is Kota Batu that once was a defence bastion in the fight against the Portuguese. It was built by Sultan Alauddin Riayat Shah II, the Second Sultan of Johor (1528-1564) in 1540 as the Johor Government Administrative Centre. This Kota Batu (Stone Fort) was built on a hill top by the left bank, downstream of Sungai Johor. Part of the fort wall is located on a steep promontory, known as Tanjung Batu. This square-shaped fort, 50 metres long and 20 metres wide contains a number of corners built specifically as a defence strategy. The fort bulwark was made from solid rocks, topped over with earth and equipped with weapon and cannons.
In 1564, Kota Batu was heavily attacked and captured by Acheh. Sultan Alauddin II was brought to Acheh where he finally meet his maker. For a period of time, appointed Sultans of Johor had to under the protectorate of Acheh. After the ascendant of Sultan Ali Jalla Abdul Jalil Riayat Shah, the fifth Sultan of Johor to the throne, His Royal Highness took the initiative to restore Kota Batu that was damaged during the Acheh attack and made it the centre of administration. Johor Lama's position as an important Malay trade centre of the time affected the Portuguese trade centre in Malacca. This resulted in Kota Batu being attacked by the Portuguese from Malacca in 1576 and 1578, but the attackers were defeated. In 1586, the Portuguese renewed their attack on the fort, but this time around they did not reach Kota Batu as the battle took place in Sungai Johor and the Portuguese troops had to retreat to Malacca.
In 1587, Sultan Ali Jalla Abdul Jalil Riayat Shah gathered a large army and attacked the Portuguese in Malacca. Due to the impenetrability of the A Famosa fort, however, the Portuguese could not be defeated. Ensuing the incident, the Portuguese hit back at Kota Batu and Johor Lama, but the forts were successfully defended by Sultan Ali's warriors. At the end of 1587, the Portuguese, with the help of soldiers from Goa, India stormed Kota Batu in a massive attack, and conquered the fort. Sultan Ali Jalla Abdul Jalil and his followers retreated and established a new administrative centre in Batu Sawar. It was since then that Kota Batu lost its significance as an important fort in the Johor Malay government.
Johor Lama, which was once the government administrative centre in the people's collective memories as a heritage civilisational umbrella of the Johor Malay Sultanate during the end of the 16th century.