Hybrid speciation is relatively common in plants compared to other well-studied groups. Polyploidy and apomixis are strongly associated with hybrid speciation, presumably due to the opportunities they provide for both reestablishing reproductive function in hybrids with incomplete chromosomal homology and creating rapid reproductive isolation in sympatry. Boechera, a species-rich genus closely related to Arabidopsis, is a particularly fertile ground for the study of hybrid speciation. Thirty-eight apomictic triploid hybrid species are currently recognized in Boechera. Recent research has shown that apomictic diploid hybrids, although very rare in angiosperms, are common in Boechera. Given this complexity, focused studies of individual species complexes are critical to understanding speciation and diagnosing biodiversity in Boechera. Here we analyze DNA sequences from seven nuclear loci and multilocus genotypes from 15 microsatellite markers in a group of closely related taxa formerly included in B. fendleri. Our results support the recognition of four species previously segregated from B. fendleri s. l., including three genetically distinct, sexual diploids (B. fendleri, B. spatifolia, and B. texana) and one apomictic triploid hybrid (B. porphyrea). We also identify four novel apomictic diploid hybrid species (B. carrizozoensis, B. centrifendleri, B. sanluisensis, and B. zephyra) and additional apomictic triploid hybrids. Our results reveal a complex network of relationships. Sexual diploid species can hybridize to form apomictic diploids, and members of these two groups can hybridize to form trigenomic, apomictic triploids.