Dudleya (Crassulaceae) is a genus of succulent perennials endemic to western North America. Interspecific relationships within Dudleya have been difficult to discern due to a lack of synapomorphic characters for the genus or subgenera, highly variable morphologies within species, and extensive polyploidy. Here we present the first molecular phylogeny of diploid members of the genus using sequences from nrDNA and cpDNA. We cloned ITS alleles from six known polyploid individuals to determine their evolutionary origin. We have been able to resolve four clades within Dudleya, but many relationships are still uncertain. Our analyses support the monophyly of the genus and show that Dudleya is more closely related to North American Sedum species of the Sedoideae subfamily than to members of its currently circumscribed subfamily, the Echeverioideae. The current subgeneric distinctions within Dudleya are polyphyletic and should be revised in future taxonomic treatments. We tested the monophyly of several highly variable species and found that D. virens, D. cymosa, and D. abramsii are polyphyletic. The ITS alleles from polyploid taxa were not variable enough to resolve polyploid origins.