Traditional accounts provide the names of several of its leaders; Sultan Hadlirin, and his wife and also successor, Ratna Kencana (Ratu Kalinyamat) (r. 1549–1579).

In 1549, Arya Penangsang, the Duke of Jipang Panolan ascended to the throne of Demak after assassinating his cousin Sunan Prawata.

Prawata younger sister Ratna Kencana, sought justice for Sunan Kudus, the teacher of Penangsang.

Disappointed, Ratna Kencana went home with her husband, Sultan Hadlirin, from Kudus to Kalinyamat only to be attacked by Penangsang's men on their way.

She urged her brother-in-law, Hadiwijaya (popularly known as Jaka Tingkir), the Duke of Pajang (Boyolali), to kill Arya Penangsang.

In 1550, Queen Regent of Jepara, Kalinyamat, alarmed at the growth of Portuguese power in the region, sent 4,000 soldiers in 40 ships to meet Sultan Johor's request to free Malacca of the Europeans.

The storm came crashing and stranded two Jepara vessels back to Malacca shore, and they fell prey to the Portuguese.

In 1568, Jepara again attacked the Strait of Malacca, combined with the forces of the Aceh Sultanate led by Alauddin al-Kahar.

Despite being beaten several times, the Portuguese had great respect for Queen Kalinyamat, dubbing her "Rainha de Japara, Senhora poderosa e rica, de kranige Dame," meaning "Queen of Jepara, a rich and powerful woman, a brave woman".