Background: Parapatric (or ‘budding’) speciation is increasingly recognized as an important phenomenon in plant evolution but its role in extreme (e.g. desert) environments is poorly documented. Aims: To test this speciation model in a hypothesized sister pair, the Southwest–North African disjunct Senecio flavus and its putative progenitor, the Namibian Desert endemic S. englerianus. Methods: Phylogenetic inferences were combined with niche divergence tests, morphometrics, and experimental-genetic approaches. We also evaluated the potential role of an African Dry-Corridor (ADC) in promoting the hypothesized northward expansion of S. flavus (from Namibia), using palaeodistribution models. Results: Belonging to an isolated (potential 'relict') clade, the two morphologically distinct species show pronounced niche divergence in Namibia and signs of digenic-epistatic hybrid incompatibility (based on F2 pollen fertility). The presence of ‘connate-fluked’ pappus hairs in S. flavus, likely increasing dispersal ability, is controlled by a single gene locus. Conclusions: Our results provide support for a rare example of ‘budding’ speciation in which a wider-ranged derivative (S. flavus) originated at the periphery of a smaller-ranged progenitor (S. englerianus) in the Namib Desert region. The Southwest–North African disjunction of S. flavus could have been established by dispersal across intermediate ADC areas during periods of (Late) Pleistocene aridification.