The dominant powers in the south were long the Makassarese kingdom of Gowa (around the port of Makassar) and the Bugis kingdom of Bone. By the mid-16th century, Gowa had established itself at the head of a major trading bloc in eastern Indonesia. The king of Gowa adopted Islam in 1605 and Bone was soon subdued, spreading Islam to the whole Bugis–Makassarese area.

The Dutch United East India Company found Gowa a considerable hindrance to its plans to monopolise the spice trade until a deal was struck with the exiled Bugis prince Arung Palakka. The Dutch sponsored Palakka’s return to Bone in 1666, prompting Bone to rise against the Makassarese. A year of fighting ensued and Sultan Hasanuddin of Gowa was forced to sign the Treaty of Bungaya in 1667, which severely reduced Gowa’s power. Bone, under Palakka, then became the supreme state of South Sulawesi.

Rivalry between Bone and the other Bugis states continually reshaped the political landscape. After their brief absence during the Napoleonic Wars, the Dutch returned to a Bugis revolt led by the queen of Bone. This was suppressed, but rebellions continued until Makassarese and Bugis resistance was finally broken in the early years of the 20th century. Unrest lingered on until the early 1930s, and revolts against the central Indonesian government occurred again in the 1950s.

The Makassarese and Bugis are staunchly Islamic and independently minded. Makassar and Pare Pare are still the first to protest when the political or economic situation is uncertain.

Today a period of prosperity has brought stability, however, and Makassar's importance continues to grow as eastern Indonesia's foremost city.