It is called the "Venice of the South"[5] due to the use of boats as primary transportation, although footbridges connect one house to another.

In the early 1900s, a man named Lailuddin ibn Jalaluddin from the area of Nunukan, Parang, Sulu was noted to be the first Tausūg to settle in Sitangkai, bringing with him his clan, wealth, and slaves.

Together with his sons and nephews, they settled, intermarried, and made alliances with the local traditional leaders and inhabitants.

During World War II, Sitangkai and Sibutu, being closer to British Borneo, was targeted by patrols and occasional raids by Japanese Imperial soldiers.

Sitangkai nowadays is still a jump off port for traditional traders from Sulu, Zamboanga, mainland Tawi-Tawi going to Sabah and Borneo.