Leucobryum boninense is an enigmatic species distributed in southeast China and islands of the northwestern Pacific and is the only species of Leucobryum known from the Bonin Islands which are typical oceanic islands. Molecular phylogenetic analysis using internal transcribed spacer (ITS) of nrDNA sequences was performed to resolve phylogenetic relationships among geographically isolated populations of L. boninense and its related species. The analysis showed that L. boninense is divided into two distinct clades, which correspond to geographical regions: an oceanic island clade (Bonin clade) and a continental region clade (Ryukyu clade). These two clades were also distinguished from each other by the ratio of the length of the prorate apex region to the whole leaf length, ecological preference and the colony habit. Plants of the Ryukyu clade proved to correspond to L. scaberulum, previously treated as a synonym of L. boninense. Molecular and morphological evidence strongly suggests that L. boninense is endemic to the Bonin Islands, and that L. scaberulum should be treated as a distinct species. Endemism of L. boninense on the oceanic islands may be result of allopatric speciation.