Between 1950 and 1965, Kahar Muzakkar led a rebellion (gerombolan) against the national government which kept South and Southeast Sulawesi in a state of civil unrest. This was linked to the Darul Islam (Islamic State) political faction and associated with the Tentara Islam Indonesia (Indonesian Islamic Army) rebellion in West Java and Aceh. During this period, Sulawesi was divided between the followers of Kahar Muzakkar and the Tentara Nasional Indonesia (National Indonesian Army), and much of Southeast Sulawesi was under the control of the rebels (Harvey 1974: 1437). The Kahar Muzakkar rebellion, commonly referred to simply as the gerombolan by the Bajo, resulted in great upheaval for the Mantigola Bajo and was responsible for large numbers settling in Mola and other settlements in the Tukang Besi Islands. From there many dispersed around eastern Indonesia.

Older generation Mola and Mantigola Bajo recall the disorder in their lives, especially during the years 1956 and 1957. Some members of the Bajo community were active supporters of the gerombolan, but their actions were opposed by the Kaledupa people and their local government. Subsequent violent reprisals and attacks by the land people forced the Bajo Mantigola to move to Sampela. These attacks took place at the instigation of local units of the Tentara Nasional Indonesia based in Kaledupa who wished to have tighter control on the Bajo. However, support for the rebellion continued, and about a year later, with further threats from the Kaledupa government, the Mantigola Bajo fled in their boats and canoes to Mola. This was done with the permission of the Wanci government which supported the rebellion (personal communication, Si Pallu, 1995). At that time, a small Bajo community of about 30 houses already existed in central Mola Utara.

During this period of unrest and upheaval, the majority of Mantigola Bajo moved to Sampela. A short while later some again fled from Mantigola and Sampela to other areas in eastern Sulawesi. Some Bajo moved to Langara village on Wowonii Island, close to Kendari. This community was later forced to flee to Kendari itself but eventually returned. Some people escaped to the villages of Matanga in the Banggai Islands and to Limbo on Kukkusang Island in Central Sulawesi. Others moved directly from Mantigola and Mola to Sulamu in Kupang Bay, and also to the Bajo village of Kabir on Pantar Island. ^[8] The community of Wuring on the north coast of Flores near Maumere was also settled by Bajo from Mantigola during the rebellion (Burningham 1993: 209). However, Si Pallu and others from Mola claim the majority of Bajo who settled in Wuring were from the island of Kabaena, east of Buton, and from Pasar Wajo on the southern coast of Buton. Suffering from similar problems, they also fled to safer areas on the outer islands.

According to the Bajo, the kampung (village) of La Manggau on Tolandono Island was established after the end of the rebellion. At that point, most of the Bajo living in Mola remained there, although some returned to Sampela and others went back to Mantigola because of its proximity to offshore coral reefs. However, since the late 1980s, the most significant migration of Bajo from Mola and Mantigola — not just male members of the community but also women and children — has been to and from the village of Pepela on the island of Roti.