Southern Sudan has a low population density, abundant land and tremendous agricultural potential. A large number of domesticated crops are grown in the region in a range of cropping systems. There are also numerous useful wild plant genetic resources. Little collecting work has been done in the region, there are few accessions from southern Sudan stored ex situ and publications on the actual and potential plant genetic resources for agriculture are sparse. The region has been a centre of civil conflict with little respite since independence in 1956. The farmers’ fields and natural environments represent in situ genebanks, which following the cessation of hostilities will become extremely important for the rehabilitation of subsistence agriculture, the promotion of cash crop production and the revitalization of the regional economy. Several wild plant species are highly nutritious and merit the attention of plant scientists. This article describes some of the domesticated, semi-domesticated and wild plant genetic resources of the area, and suggests why these are important for agricultural rehabilitation following implementation of a peace accord.