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The Macaronesian species of Euphorbia sect. Aphyllis subsect. Macaronesicae are distributed in four of the five archipelagos of Macaronesia and two mainland enclaves in Portugal and Morocco. The aims of this study are to investigate the biogeographic history of this group with AFLP and cpDNA markers, and to identify taxonomic entities within subsect. Macaronesicae based on genetic data, characterize them morphologically and infer the evolution of their diagnostic characters based on the reconstruction of ancestral character states. A continuous spatial diffusion analysis of AFLP data implicated Tenerife (central Canary Islands) as the area of origin of the group, followed by colonization of other Canarian islands and other Macaronesian archipelagos. Two dispersal events back to the mainland were also inferred. Our phylogenetic network, neighbour-joining clustering and Structure analyses of AFLP data demonstrated that species are genetically well delimited and suggested that they may have originated from a combination of allopatric speciation at broad scales (among islands) and fine scales (within islands), or possibly sympatric ecological speciation followed by more recent inter-island dispersal events. Ancestral character state reconstructions of morphological characters suggested that the ancestor of subsect. Macaronesicae was adapted to arid or mesic habitats, and traits associated with adaptation to humid habitats were acquired later. The central Canary Islands harbour the highest species diversity of this group in the Archipelago, and the highest nuclear and plastid genetic diversity. With regards to taxonomy, phylogenetic analyses and neighbour-joining clustering analyses based on AFLPs showed two clearly differentiated genetic groups, sister to each other, which correspond to the E. atropurpurea and E. lamarckii complexes formerly recognised based on morphology. Euphorbia aphylla is recovered as sister to the rest of the species, supporting its exclusion from the two complexes. Euphorbia tuckeyana is excluded from the E. lamarckii complex.