Serpula himantioides is a globally distributed wood decay fungus that causes heartwood decay in several tree species. We investigated the occurrence of S. himantioides fruiting bodies in Japan for two years and six months to characterize their biology. The fruiting bodies matured in autumn and occurred on living Chamaecyparis pisifera , Chamaecyparis obtusa , Larix kaempferi , and Cryptomeria japonica trees, as well as on dead trees and soil. Assessing three circular plots, the incidence of living trees with S. himantioides fruiting bodies was lowest in the plot with the most advanced heartwood decay. Furthermore, fruiting bodies occurred more frequently in the lower slope direction of the trunk. Analysis using the pair correlation function suggested that the spatial distribution pattern of living trees with fruiting bodies may change from intensive to random with heartwood decay progress. Finally, according to generalized linear and generalized linear mixed models, which were used to investigate the factors affecting the development of fruiting bodies in C. pisifera , C. obtusa , and L. kaempferi , no clear relationship was found between the presence or absence of fruiting bodies and heartwood decay. Thus, we suggest that fruiting bodies can occur in healthy living trees as well as in living trees in the early stages of heartwood decay.