In 1893, Lloyd Mathews built the prison. The prison idea was to send violent criminals from the Tanganyika mainland to the Prison Island. The Prison Island ended up being used as a quarantine center, instead of a prison, for yellow fever epidemics that once raged through the region. Prison Island remained in the ownership of the government which converted the newer quarantine buildings into a guest house.

The old prison still remains standing, providing shelter for some of the giant tortoises which can now only be found on this island, and the cells.

The island was once used by an Arab slave trader to contain the more troublesome slaves he had brought from the African mainland to prevent their escape before shipping them to the Arabian purchasers, or for auctioning in Zanzibar slave trade market. The slaves were dumped on the island.