Determining accurate phylogenetic relationships among the members of the woody Sonchus alliance presents challenges because of an insufficient level of molecular variation and the convergent evolution of similar morphological traits in island settings. To obtain a better resolved phylogeny and to test the potential role of hybridization and introgression, we sequenced all members of the alliance with multiple populations for the ITS of nrDNA and over 4000 base pairs of coding and noncoding regions of cpDNA. The cpDNA phylogeny is not well resolved in the core members of the alliance (i.e., subg. Dendrosonchus and genus Taeckholmia), but like the ITS tree, it has identified basal lineages of monotypic genera. The cpDNA data set was not significantly different from that of ITS, and subsequent combined analysis provided a better resolved and supported phylogeny within the alliance. The combined ML tree identified the same basal lineages, suggested nonmonophyly of Dendrosonchus and Taeckholmia, and did not support either Boulos' or Aldridge's infrasubgeneric classification system. Assessment of the role of hybridization and introgression was limited due to poor resolution in the cpDNA phylogeny. The combined analysis supports a Gran Canaria origin for the alliance and two subsequent long distance dispersal events to Madeira and Cape Verde islands.