Microdendron Broth., an eastern Asian endemic genus, was initially described based mainly on the tree-like gametophytes, but there have been several conflicting taxonomic treatments. In this study, we sequenced three DNA regions of Microdendron: the nuclear 18S, and chloroplast rbcL and trnL-F. Phylogenetic analyses indicate that Microdendron is nested within Pogonatum, suggesting that the genus should not be recognized. Additionally we found an indel in the trnL intron region shared by the two genera, which also indicates the close relationship between them. Moreover, the probable allies of Microdendron sinense Broth. within Pogonatum are suggested based on detailed investigation under the scanning electron microscope.