Metapolypodium Ching, a monotypic genus endemic to Asia mainland (SW China and its neighboring regions), is still in dispute as to its systematic position. In this paper, the phylogenetic relationships of this genus was examined based on the chloroplast DNA sequences of rbcL gene and rps4-trnS region. The rbcL genes and rps4-trnS region of M manmeiense (Christ) Ching and its closely related species were sequenced. The combined relative sequences downloaded from the GenBank, consisting of three data sets-rbcL genes, rps4-trnS region including rps4 and rps4-trnS intergenetic spacer, and the combined matrix-were used to assess relationships among them with the neighbor-joining (NJ), maximum-parsimony (MP) and Bayesian inference (BI) analyses. The phylogenetic trees based on individual sequence data and the combined data are topologically similar and reveal that M manmeiense forms a clade with the members of Polypodiodes and Polypodiastrum, which is not related to any member of Polypodium. The trees also strongly support the close relationship between M manmeiense and Polypodiodes microrhizoma (C. B. Clarke ex Baker) Ching. We should agree with Ching's opinion, recognizing Polypodium L. emend. Ching, Metapolypodium Ching, Polypodiodes Ching, Polypodiastrum Ching and Schellolepis J. Sm. as independent taxa according to the results of the present study. It is reasonable to transfer Polypodiodes microrhizoma to Metapolypodium.