The phylogenetic position of Cheilanthes brandegeei, a fern endemic to the Baja California Peninsula of Mexico, was investigated using three plastid markers (atpA, rbcL, trnG-R) and comparative morphology. Here we present robust evidence for the recognition of C. brandegeei as a member of the bommeriids, the sister clade to all other cheilanthoid ferns, and evidence that it is sister to all Bommeria species within that clade. Because of its distinctive morphology within the bommeriid clade (pinnate leaf architecture, well-developed pseudoindusium, and narrow, concolorous red-brown rhizome scales), here we propose the new genus Baja to accommodate it. Our results place Baja brandegeei together with other taxa that have a distribution in the Baja California Peninsula and mainland Mexico, rather than with hypothesized congeners in South America and Africa. Morphological characters traditionally used to classify this species as a Cheilanthes (patterns of sporangial distribution, presence of a well-developed pseudoindusium, and fractiferous petioles) are extensively homoplasious across cheilanthoids. We identify three characters that unite the newly expanded bommeriid clade: leaf indument of acicular trichomes, reticulate-cristate perispore morphology, and lateral initiation of the gametophyte meristem.