Polystichum has often been treated as a sub-cosmopolitan genus of 180-230 species (i.e., Polystichum s.l.), but several segregate genera, such as Cyrtogonellum, Cyrtomidictyum, Cyrtomium, Phanerophlebia, and Sorolepidium, have been recognized in various treatments. Together, these genera constitute the polystichoid ferns. We used a data set of 47 species of the polystichoid ferns and three outgroups, including new Rbcl sequences for six species in Asia, to address their phylogeny. Maximum-parsimony (MP) and Bayesian inference analyses were performed. The polystichoid ferns were resolved to include four major clades, the tropical American Phanerophlebia clade, the Cyrtomium s.s. clade, the Polystichum s.s. clade, and an eastern Asian clade containing Cyrtomium subser. Balansana, Cyrtogonellum, three sections of Polystichum, and Cyrtomidictyum (the BCPC clade). The Cyrtomium s.s. clade included 15 species of the genus but excluded subser. Balansana. The Polystichum s.s. clade was resolved as being monophyletic with relatively low bootstrap support, as long as Sorolepidium is included in Polystichum. The overall topology retrieved by the Bayesian analysis was similar to that of the MP tree, but generally had higher internal support. Based on the molecular phylogeny, three sections of Polystichum s.l., i.e., sect. Sphaenopolystichum, sect. Haplopolystichum, and sect. Crucifilix, may be more closely related to other members of the BCPC group. The eastern Asian BCPC group shared once-pinnate fronds, except for Polystichum sect. Sphaenopolystichum. Morphologically, once-pinnate leaf dissection and reticulate venation appear to be ancestral in the polystichoid ferns.