In a host–parasitoid system comprising mycophagous drosophilids and their parasitoids, the drosophilid and parasitoid species assemblages, host use, and the prevalence of parasitism were assessed, and the “disproportionate parasitism hypothesis” was examined with consideration given to yearly variations. The mycophagous drosophilids, their fungal food resources and parasitoids were studied by carrying out an intensive census throughout the activity seasons of 4 years (2000–2003) in Hokkaido, northern Japan. Five hymenopterous parasitoid species, four braconids and one eucoilid, were found. Parasitoids of mycophagous drosophilids are reported for the first time from Asia. Most parasitism (99.2%) was by braconids, in contrast to the dominance of eucoilids in Europe. Parasitism was restricted to the summer, and the rate was high from early July to early August every year. There was considerable yearly variation in the composition of abundant fungus, drosophilid and parasitoid species, especially between 2000 and 2001. The alternation of dominant host species was coupled with the alternation of dominant parasitoid species that differed in host use. Despite the yearly variation in the system, the most dominant host species suffered disproportionately heavy parasitism by the correspondingly dominant parasitoid species every year. The parasitism rate was positively correlated with the relative host abundance. This thus indicates that the disproportionate parasitism mechanism may operate, via which species coexistence is promoted by a higher rate of parasitism of the dominant species.