Southern Africa is subject to strong interannual summer rainfall extremes associated with modes of climate variability. Interaction between these modes and the climate change signal make improving understanding of their future operation and links with southern African rainfall a priority. This paper examines future southern African summer rainfall variability related to a meridional dipole mode of southwest Indian Ocean SST variability (the SWIOD) in coupled climate model HadCM3. The SWIOD is central to southern African rainfall in a 1000-year control simulation, and remains so during the twenty-first century under two different CO2 forcing scenarios: SRES A2 and B1. Future rainfall variability connected with this mode is found to be sensitive to the emissions pathway, particularly in the second half of the century. Flooding episodes with anomalies near 4 mm day−1 in already wet regions and which are unprecedented in a 1000 year control run are simulated under A2 SRES forcing.