There is little available data on the biogeography of myxomycetes at the regional scale within any given climate zone. To investigate the geographical distribution of these protozoans, we focused on corticolous myxomycetes associated with the bark of Cryptomeria japonica trees, which we sampled extensively throughout Japan. Myxomycete sporophores developed in 73% of 2244 moist-chamber cultures of 188 bark samples from 24 regions, including 31 species. The most abundant species were Paradiacheopsis rigida and Cribraria confusa, which accounted for over 20% of all myxomycetes sampled. Non-metric multidimensional scaling was used to analyze the distribution of myxomycetes in relation to geographical variables and bark pH. The distribution of myxomycetes was influenced by altitude, temperature and bark pH. Temperature gradients and relative abundance of species were negatively correlated in P. rigida and Comatricha laxa and positively correlated in C. confusa, Macbrideora cornea, and Diderma chondrioderma. Bark pH was also positively correlated with the relative abundance of C. confusa, D. chondrioderma, and Physarum nutans and negatively correlated with that of P. rigida, P. cribrata, Enerthnema papillatum, and E. melanospermum. Geographical distribution of corticolous myxomycete communities was determined based on temperature and bark pH, which acted as local barriers in our study area.