This paper presents the first phylogenetic hypotheses for the 20 species of Cistus based on plastid (trnL-trnF, matK) and nuclear (ITS) DNA sequence data. Phylogenetic relationships reveal that: (1) Halimium and Cistus form a cohesive, natural group; (2) two major lineages of purple-flowered and white-flowered species are defined, except for the purple-flowered C. parviflorus; (3) monophyly of conspecific populations is congruent with the circumscription of species. Topological congruence between nuclear and plastid phylogenies does not support a predominant reticulate system of evolution in Cistus. Reconstruction of character evolution suggests an increment of number of fruit valves in the Cistaceae from 3 to 12 in a unidirectional manner. In contrast, reproductive characters, such as sepal number, petal color, and style length, evolved multiple times in the course of evolution. A single colonization of Cistus into the Canary Islands appears to be responsible for a lineage of four species sharing a most recent common ancestor with five sepals, purple flowers, styles as long as stamens, and five fruit valves. Species diversity in Cistus (14) and Halimium (8), coupled with sister-group relationships and molecular divergence, lead us to suggest the western Mediterranean as a major center of present-day differentiation, but paleobotanical data indicate an earlier formation of the Cistus-Halimium assemblage in different areas.