The Sonoran Desert Clade milkweeds have very unusual traits, including species that are nearly leafless and shrubby. This clade includes 9 species for which we estimate a phylogenetic tree and use this information to better understand why species within this clade are diverging from their ancestral species. To do this we use plastid genomes to find genetic differences among the species. We assembled and aligned plastomes for multiple individuals of each species and found the maximum likelihood phylogenic tree. From the results we found that the Sonoran Desert Clade forms one clade rather than multiple. We found interesting relations between some of the species within the Sonoran Desert Clade. There was hybridization that we found within the results. This will help us further our study on the evolution of the Asclepias species.