We examined host abundance of limoniid flies between Agaricales (gill mushrooms) and Aphyllophorales (non-gilled fungi) and the importance of these flies as phoronts of mites inhabiting these fungal orders. Fungal sporophores were collected around transects established in five different-aged (13 to more than 100 years) forest stands from spring to fall in temperate forests of Japan. Limoniid flies and mites were collected from sporophores during transect sampling and reared from sporophores in the laboratory. All 11 limoniid species reared from sporophores used Aphyllophorales and six of these limoniid species also used Agaricales as their hosts. The total number of limoniid flies reared from Aphyllophorales was approximately seven times that reared from Agaricales. Eight of 15 Aphyllophorales species yielded multiple limoniid species. We conclude that Aphyllophorales are more important as hosts for fungivorous limoniid flies than Agaricales. Even a single fungal species can support more than one limoniid or mite species. One or two limoniid species are phoronts for one to three mite species inhabiting sporophores of Agaricales and Aphyllophorales. These flies have an important role as phoronts for some mite genera inhabiting fungal sporophores.