Southern Sudan is in the midst of a massive transformation from a society ravaged by fifty years of war to a democracy governed by the rule of law and a modern judiciary. Violence, especially against women, remains rampant and police and the justice system remain largely unable to meet the needs of communities. In this context traditional or customary justice systems composed of chiefs and clan headsmen continue to resolve disputes and apply traditional practices of restorative justice. The South is on a quest for modernity in its institutions but is it at risk of destroying these already functioning traditional systems of dispute resolution in its rush to develop? There is a need for more analysis of the harms and benefits traditional courts provide. And while legal pluralism does not have a perfect track record in Africa there might be important lessons that can be applied to the Southern Sudan context. This article combines reflections on previous African experiences with a recent study of customary courts in Southern Sudan. The research reveals a contrast between structural benefits of customary courts and chronic miscarriages of justice for violence against women. The article builds on this analysis to suggest reforms through a balanced bottom-up and top-down approach, including a potential framework for a pluralist justice system.