The rare sequestrate fungus, Chamonixia caespitosa, is known to occur in Europe and North America. The species has also been reported once from China, but the precise information on its occurrence in Asia is unknown. We collected fruiting bodies of C. caespitosa in a subalpine coniferous forest in central Japan. The internal transcribed spacer phylogeny shows that the Japanese collections are more closely related to one of the North American infraspecific lineages than to the European lineage. Thus, these Japanese collections could be a missing link in the phylogeography of the genus Chamonixia.