From 1898 to 1956 South Sudan was part of the joint administration of the Anglo-Egyptian Sudan. Britain had ruled the South since 1877 and Egypt the North since 1821. The North was an Arabic/Muslim territory whereas the South was African/Christian/Traditional religions.
Britain had wanted to join the territory of what is largely South Sudan with Uganda. This was opposed by Arab and other interests and in 1947 the Juba Conference effectively unified northern and southern Sudan against strong the opposition of the South.
In 1955, prior to independence, a mutiny in the South started a First Sudanese Civil War, which ended in 1972 but soon re-ignited as the Second Sudanese Civil War.
In 2005, Juba (reportedly founded by Greek traders in 1922) rather than Rumbek became the capital of the Autonomous Government of Southern Sudan. Juba then became the new country's capital.