The study of evolution in deserts has been hindered by the lack of reliable phylogenies for major desert plant groups. Cacti are conspicuous members of the American deserts but notorious for convergent evolution of morphological characters that has thwarted phylogenetic analysis. We constructed a phylogeny of the Cactaceae based on DNA sequence comparisons from 6,000 chloroplast nucleotides and the nuclear Internal Transcribed Spacer. Sampling included more than 120 species from all currently recognized subfamilies and tribes of the family and outgroups from the Portulacaceae. Parsimony analysis resulted in a well-resolved strict consensus tree with strong to moderate bootstrap support for most branches. Some previously hypothesized relationships are supported by these results, however many others are not and provide new insights for improved taxonomy and classification in the Cactaceae. Cacti inhabit warm deserts and cold, temperate deserts and tropical, as well as other habitat types, making them uniquely useful for comparative studies, and for understanding historical connections between arid regions.

Key words: Cactaceae, deserts, molecular systematics