The following is a list of ecoregions in South Sudan, as identified by the Worldwide Fund for Nature (WWF).

by major habitat type

• East African montane forests

• East Sudanian savanna
• Northern Acacia–Commiphora bushlands and thickets
• Northern Congolian forest–savanna mosaic
• Sahelian Acacia savanna
• Victoria Basin forest–savanna mosaic

• Saharan flooded grasslands

• Upper Nile
• Lake Turkana

• Burgess, Neil, Jennifer D’Amico Hales, Emma Underwood (2004). Terrestrial Ecoregions of Africa and Madagascar: A Conservation Assessment. Island Press, Washington DC.
• Thieme, Michelle L. (2005). Freshwater Ecoregions of Africa and Madagascar: A Conservation Assessment. Island Press, Washington DC.