Phylogenetic relationships were reconstructed using molecular (nrDNA ITS and rpl16) and morphological data for eight species in three sections (Leptosyne, Pugiopappus, and Tuckermannia) of Coreopsis that are almost exclusively restricted to California. Parsimony analyses were conducted on each of three data partitions (cpDNA, ITS, and morphology) and congruence between these topologies and data sets was assessed by inspecting the topology for “hard” incongruence and via the partition homogeneity test (PHT). The individual topologies were largely congruent (i.e., lacking “hard” incongruence), with the exception of the placement of C. calliopsidea by analyses of morphological data. Because the two molecular data sets are generally in agreement regarding the placement of this taxon, the morphological data for C. calliopsidea were excluded and a PHT test indicated no significant heterogeneity among the molecular partitions. A combined analysis supports the monophyly of the eight California species and of sections Tuckermannia and Leptosyne; however, section Pugiopappus is not monophyletic. This latter section as traditionally defined includes species that display an annual habit and dimorphic cypselae. Examining the evolution of these two features in light of the phylogeny indicates that the annual habit has either arisen twice or arose once with reversal to perenniality, and that dimorphic cypselae originated twice. The evolution of pubescent fruits and pappus scales is more complex. The three alternative reconstructions indicate that these features could either be ancestral, represent three independent gains, or result from a single gain followed by two losses.