In this paper, we examined how regional integration affected cross-border M&A in Africa for the period 2000 to 2014 using a structural gravity model. We found that customs unions in Africa, specifically Southern Africa Customs Union (SACU) and the East African Community (EAC) are significant drivers of M&A by firms from within the unions but not those from outside, perhaps due to their relatively small size. This finding suggests that the depth of regional integration determines intra-regional M&A flows in Africa. Findings from this paper suggest that African governments need to strengthen the existing regional integration arrangements, as the case of SACU and EAC indicates, to benefit from intra-African cross-border M&A flows.