Sultan Alauddin Riayat Shah II ibni Almarhum Sultan Mahmud Shah (died 1564) was the first Sultan of Johor. He ruled Johor from 1528 to 1564. He founded the Johor Sultanate following the fall of Malacca to the Portuguese in 1511. He was the second son of Mahmud Shah of Malacca. Thus, Johor was a successor state of Malacca and Johor's sultans follow the numbering system of Malacca. Throughout his reign, he faced constant threats from the Portuguese as well as the emerging Aceh Sultanate.

In 1529, Alauddin Riayat founded his first capital in Hujung Tanah, known as Pekan Tua, 11 km upriver from Kota Tinggi, following the death of his father. A river fort, Kota Kara was also founded down the river. In 1535, about 400 Portuguese troops led by Estêvão da Gama invaded Johor. Kota Kara was bombarded but the Malays withstood the attack. After a few days, Portuguese troops landed and bombarded the fort but they also had to retreat. Their morale boosted by this initial success, the Malays left their fort and launched a counter-attack on the Portuguese. However, the Malays were scattered by the crossfire of the Portuguese which resulted in the capturing of the fort and its burning by the Portuguese.

Alauddin Riayat retreated upstream the Johor River to Sayong Pinang. His official, Seri Nara Diraja, died in Sayong Pinang. Alauddin Riayat returned to Pekan Tua after a short period and rebuilt it. Pekan Tua was attacked by 400 Portuguese troops under Estêvão da Gama again because his brother, Paulo da Gama, and about 30 other Portuguese troops were killed by Malays. Following this attack, a peace treaty was signed between Johor and the Portuguese.

In 1540, Alauddin Riayat Shah moved his capital to Johor Lama, which is closer to the estuary of Johor River.

...
Wikipedia