Boecherais a model genus that is of particular interest for understanding apomixis due to the presence of numerous apomictic diploid lineages that are tightly correlated with hybridisation events.Boecheraincludes many narrowly distributed endemics and apomictic hybrid lineages that obscure morphological boundaries amongst taxa. In this study, we focus on theBoecherasuffrutescenscomplex, a phylogenetically well-supported but taxonomically complex north-western United States clade whose diploid species currently include the widespreadB.suffrutescensand two narrowly distributed serpentine endemics,B.constanceiandB.rollei. Using a 15-locus microsatellite dataset, we infer ploidy and sexual vs. apomictic reproduction for all individuals and then assess species limits for all sexual diploid samples. Our results support the recognition ofB.rolleiandB.constanceias distinct species and reveal three divergent sexual diploid lineages withinB.suffrutescenssensu lato. The latter three lineages exhibit geographic, genetic and morphological coherence and consequently warrant recognition at the species rank. These includeBoecherasuffrutescenss.s., which is restricted to Idaho and eastern Oregon,Boecherabotulifructa, a newly described species distributed along the Cascade Mountain Province from Lassen County, California north to Deschutes County, Oregon and the heretofore dismissed speciesBoecheraduriuscula(basionym ≡Arabisduriuscula), which occurs along the Sierra Nevada Province from Plumas County southwards to Fresno County, California. Our data also reveal substructure inB.constanceithat is likely attributable to the highly fragmented distribution of its serpentine habitat. This refined taxonomic framework for theB.suffrutescenscomplex enhancesBoecheraas a model system, adds to our knowledge of speciation in edaphically extreme environments and provides information on ongoing conservation efforts for these taxa.