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We examine patterns of variation in 12 continuous morphological traits, chloroplast DNA sequences from 10 intergenic spacer regions (petA-psbJ, psbk-trnS, psbM-trnD, rpob-trnC, trnC-trnD, trnGCU-trnG2S, trnFM-trnUGA, atpF-atpH, trnT-trnD, trnQ-psbk), atpF, and rpl16, and Amplified Fragment Length Polymorphism (AFLP) genetic markers in Sclerocactus glaucus sensu lato (= S. brevispinus, S. glaucus, and S. wetlandicus), a complex that historically has been considered conspecific and afforded protection under the Endangered Species Act. This complex is considered to represent three different species by some authors. We describe the expected patterns of morphological, DNA, and AFLP variation under the conditions that (a) the complex is a single species, and (b) that there are three antonymous species. We show that morphological evidence is consistent with the presence of three significantly different morphological species. Chloroplast DNA sequences provide evidence that the populations of S. glaucus (restricted to Colorado) are a lineage distinct from the populations of S. brevispinus and S. wetlandicus (restricted to Utah). AFLP genetic markers reveal significant genetic divergence among S. brevispinus, S. glaucus, and S. wetlandicus. Equally important, there is greater divergence among species than among populations within the species. The three sources of evidence all support the presence of three species and not a single species. These results indicate that protection of S. glaucus as a threatened species under the Endangered Species Act, as historically prescribed, includes populations of three species, two in Utah (S. brevispinus and S. wetlandicus) and one in Colorado (S. glaucus).