Rock daisies (Perityleae; Compositae) are a diverse clade of seven genera and ca. 84 minimum-rank taxa that mostly occur as narrow endemics on sheer rock-cliffs throughout the southwest U.S. and northern Mexico. Taxonomy of Perityleae has traditionally been based on morphology and cytogenetics. To test taxonomic hypotheses and provide new perspective on the evolution of characters emphasized in past treatments, we present the first densely sampled molecular phylogenies of Perityleae and reconstruct trait and chromosome evolution. We inferred phylogenetic trees from whole chloroplast genomes, nuclear ribosomal cistrons, and hundreds of low-copy nuclear genes using genome skimming and target-capture. Discordance between sources of molecular data suggests an underappreciated history of hybridization in Perityleae. Phylogenies support the monophyly of subtribe Peritylinae, a distinctive group possessing a four-lobed disc corolla; however, all of the phylogenetic trees generated in this study reject the monophyly of the most species-rich genus, Perityle. Using reversible jump MCMC, our results suggest that morphological characters traditionally used to classify members of Perityleae have evolved multiple times within the group. A base chromosome number of x=9 gave rise to higher base numbers in subtribe Peritylinae (x=12, 13, 16, 17, 18 and 19) through polyploidization followed by ascending or descending dysploidy. Most taxa constitute a monophyletic lineage with a base chromosome number of x=17, with multiple neo-polyploidization events. These results demonstrate the advantages and obstacles to next-generation sequencing approaches in synantherology while laying the foundation for taxonomic revision and comparative study of the evolutionary ecology of Perityleae.