Using 11 microsatellite markers, we investigated the allelic variation and genetic structure of Cryptomeria japonica, across most of its natural distribution. The markers displayed high levels of polymorphism (average gene diversity=0.77, average number of alleles=24.0), in sharp contrast to the lower levels of polymorphism found in allozyme and cleaved amplified polymorphic sequence markers in previous studies. Little genetic differentiation was found among populations (F(ST)=0.028, P<0.001), probably because the species is wind-pollinated and long-lived. No clear relationship between Nei's genetic distances and geographical locations of the populations were found using the principal coordinate and unweighted pair-group method with arithmetic averaging analyses. The lack of such trends might be due partly to microsatellite homoplasy arising from mutation blurring the genealogical record. However, there was a trend towards high allelic diversity in five populations (Ashitaka, Ashiu, Oki-Island, Yakushima-Island-1 and -2), which are very close to, or in, refugial areas of the last glacial period as defined by Tsukada based on pollen analysis data and current climatic divisions. We postulate that these refugial populations might have been less affected by genetic drift than the other populations due to their relatively large size.