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Storm disturbance has a huge impact on subalpine forest ecosystems. Evaluating the long-term effects and mechanisms of storm disturbance is of great significance for conservation of subalpine forests as frequency and intensity of storms are increasing because of the climate change. Species of subalpine conifer tree genera such as Picea and Tsuga need coarse woody debris (CWD) such as logs and stumps for seedling colonization; thus, their establishment is greatly affected by the condition of CWD, which largely depends on the activity of fungal decomposer communities and saproxylic bryophyte communities. Because the process of CWD decay and associated ecological succession is known to take several decades in subalpine forests, we hypothesized that storm disturbance has long-lasting effects on fungal communities, their wood decay function, saproxylic bryophyte communities, and seedling establishment. To test this hypothesis, we surveyed fungal, bryophyte, and seedling communities at forest sites that had been disturbed by a large typhoon 55 years ago and compared them with those of surrounding undisturbed coniferous forest in central Japan. Contrary to our hypothesis, Illumina sequencing for the fungal ITS1 region in rDNA obtained from wood samples did not show that past disturbance had an obvious effect on current fungal communities. Also, the frequencies of occurrence of various wood decay types were not significantly different between disturbed and undisturbed plots. However, disturbance affected bryophyte communities, which had strong effects on the seedling densities of Picea jezoensis var. hondoensis, Tsuga diversifolia, and Betula spp. These results suggest that the previous typhoon disturbance in the focal area had long-lasting effects on biotic interactions and seedling regeneration on CWD, but these effects might not be attributable to the impacts of disturbance on CWD fungal communities and their wood decay function.