Makassar Strait is a strait between the islands of Borneo and Sulawesi in Indonesia. To the north it joins the Celebes Sea, while to the south it meets the Java Sea.

The Mahakam River of Borneo empties into the strait.

Ports along the strait include Balikpapan on Borneo, and Ujung Pandang and Palu on Sulawesi. The city of Samarinda is 48 km (30 mi) from the strait, along the Mahakam.