Euphorbia polycarpa (Euphorbia subg. Chamaesyce sect. Anisophyllum) is one of the most common species of the Sonoran Desert. It exhibits a wide range of morphological variation and has been considered as a taxonomic complex. Since the late nineteenth century more than seven varieties have been described for the complex, some with very restricted distributions. Because of morphological intergrades present in the complex, there has been much confusion among taxonomists, and it became necessary to clarify the taxonomy of this complex using molecular phylogenetic evidence in addition to morphology alone. In this paper we reconstruct the phylogenetic relationships for the E. polycarpa complex based on molecular information from the psbA-trnH and ITS spacers, using Bayesian inference. Morphology was compared with phylogenetic results, and we also explored geographic patterns of the varieties of the complex, as well as closely related species of Euphorbia sect. Anisophyllum. Taking into account the results obtained, we propose that E. polycarpa is treated as a single, highly variable species. Given the incongruities among morphology, geography, and evolutionary history inferred from molecular data, we do not recognize any of the varieties proposed previously. The phylogeny presented shows three well-supported putative lineages and suggest a complex evolutionary history within E. polycarpa.