AbstractAimThe disjunct distribution patterns of sister taxa can arise when previously continuous distribution ranges are fragmented by environmental changes such as major climatic events. Populations become isolated on either side of the newly established environmental barrier, and absence of gene flow promotes allopatric speciation, in a process that is known as ecological vicariance. If climate change altered the ancestral range gradually, such as along temporal temperature or moisture gradients, the age of divergence of disjunct species should be related to the lineage tolerance to climatic conditions. Here, we investigate this hypothesis using as a study model the African Rand Flora, a continental‐scale floristic pattern that relates sister taxa distributed on either side of the Saharan Desert.LocationAfrica, Macaronesia, Mediterranean Basin and the Middle East.MethodsWe estimated the extant climatic tolerances of 14 Rand Flora lineages based on present occurrence data, and correlated the phylogenetic age of divergence between vicariant clades. We tested whether the tempo of the vicariance in the Rand Flora lineages was associated with the average values of their climatic niches in agreement with niche‐driven divergence. We hindcasted species ranges using species distribution models combined with palaeoclimate simulations to infer the potential distribution of each lineage's ancestors.ResultsWe found a positive relationship between the lineage temperature niche and the age of the Rand Flora disjunction: lineages with subtropical affinities diverged first, whereas those with a higher tolerance to drier conditions (temperate or sub‐xeric adaptations) exhibited younger disjunctions. The range reconstructions showed the existence of climatic corridors south of the Sahara in the wetter Late Miocene, which became interrupted during the mid‐Pliocene warming event.Main conclusionsOur results suggest that climate change leading to the formation of the Sahara Desert drove Rand Flora lineages divergences along a temporal sequence that matched the climatic niche of species.