Ever since Indonesia achieved independence in 1945 the government in Jakarta has faced a constant struggle to keep the nation's 14,000 islands together.
Click on the map below for some of the main areas of conflict.
Much of Indonesia's regional violence is due to cultural or religious differences, pitting Muslims against Christians or one ethnic group against another.
Other areas want nothing less than full independence from Jakarta, and their hopes were raised when East Timor became a separate country in May 2002.
Indonesia's first two presidents, Sukarno and Suharto, ruled this disparate group of islands with iron fists and support from the armed forces.
Since the end of the Suharto regime, in 1998, reforms have led to a weakening of the previously all-powerful military.
Some say this is a long-overdue development to appease those who want increased regional autonomy.
But others say a weakened army has reduced Jakarta's ability to quell regional unrest.