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; it is sister to all Bommeria. 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.