Much work has been done on the endemic floras of Madeira and the Canary Islands but little is known about the origin and diversification of endemic plants of the Cape Verde archipelago. In this study we focus on the three endemic species of the genus Echium L. (Boraginaceae) in Cape Verde. Phylogenetic analyses based on nuclear (ITS1, ITS2) and plastid (trnT-L, trnL-F, rps16, psal-deed) DNA markers produced similar topologies that suggest a recent single colonization event in the Cape Verde archipelago, with subsequent diversification during the Pleistocene (<1.8 Ma). All datasets recovered a split between the "southern" (E. hypertropicum, E. vulcanorum) and "northern" (E. stenosiphon s.l.) island species, and suggest that habitat adaptation and inter-island colonization played a prominent role in the evolution of Echium in Cape Verde. Implications of the results are discussed in the context of the biogeography of the Macaronesian Islands. The northern island species are classified into three distinct subspecies, one for each of the northern islands: E. stenosiphon subsp. stenosiphon endemic to Sao Vicente, subsp. lindbergii endemic to Santo Antao, and subsp. glabrescens endemic to Sao Nicolau