New genome sequencing techniques are enabling phylogenetic studies to scale-up from using a handful of loci to hundreds or thousands of loci from throughout the genome. In this study, we use targeted sequence capture (TSC) data from 540 ultraconserved elements and 44 protein-coding genes to estimate the phylogenetic relationships among all 17 species of horned lizards in the genus Phrynosoma. Previous molecular phylogenetic analyses of Phrynosoma based on a few nuclear genes, restriction site associated DNA (RAD) sequencing, or mitochondrial DNA (mtDNA) have produced conflicting relationships. Some of these conflicts are likely the result of rapid speciation at the start of Phrynosoma diversification, whereas other examples of gene tree discordance appear to be caused by active and residual traces of hybridization. Concatenation and coalescent-based species tree phylogenetic analyses of these new TSC data support the same topology, and a divergence dating analysis suggests that the Phrynosoma crown group is up to 30 million years old. The new phylogenomic tree supports the recognition of four main clades within Phrynosoma, including Anota (P. mcallii, P. solare, and the P. coronatum complex), Doliosaurus (P. modestum, P. goodei, and P. platyrhinos), Tapaja (P. ditmarsi, P. douglasii, P. hernandesi, and P. orbiculare), and Brevicauda (P. braconnieri, P. sherbrookei, and P. taurus). The phylogeny provides strong support for the relationships among all species of Phrynosoma and provides a robust new framework for conducting comparative analyses.