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We investigate biogeographical, regional and sub-regional-scale responses of scarabaeine dung beetles to late Cenozoic changes in edaphic and climatic character that created a Savanna/Karoo transition zone in the Northern Cape, South Africa. Across a 50 200 km(2) study area, the Northern Cape species pool comprised six biogeographical groups defined from distribution across southern Africa. These species groups contributed in different proportions to five regional assemblages defined from structural differences across the transition zone. Towards transition zone peripheries, regional assemblage structure was more strongly correlated to sandiness dating from Miocene to Pliocene deposition (Kalahari), aridity dating from Pliocene to Pleistocene climatic change ( Bushmanland Karoo), or cooler temperatures dating from Miocene to Pliocene uplift (Upper Karoo). Correlates of sub-regional assemblages trended to intensification of dominant drivers towards regional peripheries. Drivers of central transition zone, regional assemblages (’Gariep Karoo’, ’Gariep Stony Karoo’) showed no dominance. Biogeographically, endemism dominates the Northern Cape transition zone: south-west arid groups in Nama Karoo regions; Kalahari plus north-east savanna groups in the Kalahari. Regionally, transition drives assemblage structure: unique variance, 60% in the Kalahari, 21-30% in four Nama Karoo regions; shared variance (overlap), 25-65% between Kalahari and warmer Karoo regions, 11-71% between mainly cooler Karoo regions. c 2016 The Linnean Society of London, Biological Journal of the Linnean Society, 2016, 119, 329-347.