Colysis (Polypodiaceae) is a genus with approximately 30 species found in Asia, Africa, Australia (restricted to Queensland), and New Guinea, including ca. 15 species in China. The systematic position and taxonomic circumscription of Colysis has remained unresolved since its establishment in 1849. In this work we retrieved the chloroplast DNA sequences rbcL and rps4-trnS for Colysis and its closely related taxa. Two data sets-the rbcL gene and rps4-trnS region (including both the rps4 gene and the rps4-trnS intergenic spacer) were analyzed separately and together to assess phylogenetic relationships using maximum parsimony (MP) and Bayesian inference (BI). Both separate and combined data sets yielded largely congruent results and revealed that Colysis formed a well-supported monophyletic group with Leptochilus Kaulf. (here designated as the C-L Clade). Two Leptochilus species fell into different subclades of the C-L clade. Phymatosorus Pic. Serm. formed a distinct lineage in the current analysis. The genus Microsorum Link, as traditionally defined, was polyphyletic; while M linguiforme, M varians, and M pustulatum clustered with Malaysian Lecanopteris, other microsorums were isolated in different clades. Our phylogenetic analysis suggests that Leptochilus and Colysis may better be treated as one genus.