Many African countries face escalating challenges of increasing disaster risk and anticipated impacts of climate change. Although disaster risk reduction (DRR) and climate change adaptation (CCA) are tightly linked and comprising virtually identical practices in vulnerable countries in Southern Africa, research has identified parallel governance structures across the region. This study applied comparative case study research, based on 27 semi-structured interviews, to investigate the reasons for and effects of such parallel structures for DRR and CCA in Botswana, Mozambique, the Seychelles, Tanzania and Zambia. It revealed overwhelmingly negative effects in terms of unclear mandates and leadership, uncoordinated efforts, duplication of efforts, suboptimal use of resources and competition over resources and control. The study identified both external reasons for the parallel structures, in terms of global or international initiatives or incentives, and internal reasons, with regard to the history and quality of the governance structures. Although the identified negative effects are common to a range of complex nexuses, there is a clear distinction with the DRR–CCA nexus comprising virtually indistinguishable practices in Southern Africa. There is, as such, no practical reason for keeping them apart. The parallel structures for DRR and CCA are instead the result of pervasive institutionalisation across the region, driven by coercive, mimetic and normative pressures coming from both within and abroad. Although much point to the difficulties of changing the studied institutional arrangements, these parallel structures for DRR and CCA must be addressed if the populations in Southern Africa are to enjoy safety and sustainable development.