Fremontias, or flannel bushes (Fremontodendron), are a distinctive element of California's chaparral communities. Fremontodendron decumbens is only known from a few populations in gabbro soil plant communities of the Sierra Nevada foothills in El Dorado County. Although a recovery plan for these communities has been drafted, the long-term management of F. decumbens is complicated by its treatment as a subspecies of the more widespread F. californicum, and by the recent discovery of additional populations of decumbent plants in Yuba and Nevada Counties that are not easily assigned to either F. californicum or F. decumbens. Genetic relationships among 5 populations, including F. californicum, F. decumbens, and the decumbent plants in Yuba County, were ascertained using AFLP markers. Principal coordinates and population structure analyses of the AFLP data showed that F. decumbens is genetically distinguishable from the populations of F. californicum that we sampled. This distinction, coupled with its unique morphology and ecology, support the treatment of F. decumbens as a species and promote its continued conservation as a rare and unique element of plant communities on gabbro soils in the Sierra Nevada. The decumbent Yuba County population shared a number of alleles with F. californicum and F. decumbens and the analyses did not clearly distinguish its taxonomic relationships. It is possible that this population represents an historical hybrid between F. californicum and F. decumbens. A resolution of the taxonomic position of the decumbent Yuba County populations will require more thorough sampling of F. californicum but the presence of unique alleles in this population suggests that it also should be conserved.