Nucleotide sequence variation in the ITS1‐5.8S‐ITS2 region of nuclear ribosomal DNA and in the trnL‐trnF region of chloroplast DNA from 49 specimens of Bryopteris (Lejeuneaceae) and three outgroup species was analyzed using maximum parsimony and maximum likelihood. The nrITS region exhibits high levels of nucleotide variation, whereas the trnL‐trnF region is fairly similar among samples of the same species. Three major clades were found corresponding to the Neotropical species Bryopteris diffusa and Bryopteris filicina, as well as Bryopteris gaudichaudii from the Malagasy region. Morphological characters utilized in earlier studies to distinguish five microspecies within B. filicina are diffusely distributed in the molecular topologies and do not trace monophyletic lineages. The nrITS signal suggests a separation into two biogeographically defined B. filicina clades—one mainly Andean clade and one mainly northern Neotropical clade—but these clades lack statistical support. The two clades can possibly be e...