This chapter explains the institutional deadlock and recent disruption of regional market integration in southern Africa. It contributes to the theory-driven debate on regionalism outside Europe by taking external agency explicitly into consideration as suggested in the recent debate. The chapter focuses on the macro level of international relations, with states and regional organizations being the central actors. It reviews that regional economic integration in the less developed South is for structural reasons generally more prone to interfering external agency than in the more developed north. The chapter explores against the background of the ongoing negotiations of Economic Partnership Agreements (EPA) with the European Union (EU) both African regional organizations are internally fragmented into various country groupings that are about to conclude divergent EPAs. It presents case studies on Southern African Development Community (SADC) and Southern African Customs Union (SACU) which explains the interfering impact of external agency on regional integration in the South.