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Phylogeography above the species level is a powerful tool for investigating patterns and processes at the boundary between divergent and reticulate relationships. We examined the evolutionary history of perennial species in the western Mediterranean composite genus Helminthotheca using DNA sequence and fingerprint data. The origin of the group was in western North Africa, a region of intensive Pleistocene speciation. From here it expanded to the Iberian Peninsula and Sicily. The inferred evolutionary history is compatible with the concept of ecogeographic isolation, which refers to the fact that geographic ranges of diverging lineages are largely non-overlapping due to adaptive differentiation., In phylogeography, DNA sequence and fingerprint data at the population level are used to infer evolutionary histories of species. Phylogeography above the species level is concerned with the genealogical aspects of divergent lineages. Here, we present a phylogeographic study to examine the evolutionary history of a western Mediterranean composite, focusing on the perennial species of Helminthotheca (Asteraceae, Cichorieae). We used molecular markers (amplified fragment length polymorphism (AFLP), internal transcribed spacer and plastid DNA sequences) to infer relationships among populations throughout the distributional range of the group. Interpretation is aided by biogeographic and molecular clock analyses. Four coherent entities are revealed by Bayesian mixture clustering of AFLP data, which correspond to taxa previously recognized at the rank of subspecies. The origin of the group was in western North Africa, from where it expanded across the Strait of Gibraltar to the Iberian Peninsula and across the Strait of Sicily to Sicily. Pleistocene lineage divergence is inferred within western North Africa as well as within the western Iberian region. The existence of the four entities as discrete evolutionary lineages suggests that they should be elevated to the rank of species, yielding H. aculeata, H. comosa, H. maroccana and H. spinosa, whereby the latter two necessitate new combinations.