<em>Cryptomeria japonica</em>, commonly known as Japanese cedar, is now widely distributed from glacial refuges to the entire Japanese archipelago, after the last ice age. The bark surface provides a habitat for many corticolous myxomycetes. Although corticolous myxomycetes are known to prefer tree species, the association between myxomycete distribution and host tree (<em>C. japonica</em>) divergence across the refuges has not been investigated. In this study, myxomycete communities in five refuges were assessed and compared with those in 14 peripheral areas. Bark samples were collected from at least 10 trees per site and were subjected to the moist chamber culture method (10 Petri dishes per tree) to examine the myxomycete fruiting bodies strictly. Environmental variables such as geographical location, climate condition, and bark traits (tree size, bark pH, and electric conductivity) were measured. Fruiting bodies appeared in 91% of the cultures, and 32 taxa (31 species and one varie ty) were recorded. Comparison of the communities between refuges and peripheral sites showed six myxomycete species, Arcyria cinerea, <em>Macbrideola argentea</em>, <em>Cribraria minutissima</em>, <em>Clastoderma debaryanum</em>, <em>Physarum viride</em> and <em>Physarum pusillum</em>, were significantly more abundant in the refuges and these communities preserved higher species diversity. By nonmetric multidimensional scaling, the communities in the Pacific side and the Sea of Japan side were ordered based on snow cover depth, in a pattern similar to the phylogenetic distribution of the host tree. Myxomycete groups were identified in the northern region, the Sea of Japan region, and the southern region (including Yakushima Island) of Japan. Thus, the refugial tree populations preserved the myxomycete species diversity on their bark and functioned as an important hotspot for myxomycetes. The distribution of corticolous myxomycetes was associated with the diversification and biogeographical distribution history of their host tree, <em>C. japonica</em>.