Phylogenetic relationships of the SE Asiatic genus Christiopteris were explored by comparative analysis of sequence variation of four chloroplast genome regions that were successfully used in previous phylogenetic studies of Polypodiaceae. This small genus is nested within the drynarioid ferns, as recovered with good support by each of the methods applied to reconstruct the phylogeny, including maximum parsimony and maximum likelihood. The placement of Christiopteris within drynarioids enhances the need of a new generic classification for these ferns because Dynaria is paraphyletic in its current circumscription. Two alternative classifications are discussed. The results also support the hypotheses that leaf differentiation into litre collectors and trophosporophylls is an autapomorphy of drynarioid ferns and that SE Asia is the putative ancestral area for drynarioid and selligueoid ferns. Two clades of drynarioid ferns colonized Eastern Malesia independently, but only one of these colonization events created species endemic to New Guinea. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 157, 645–656.