Myxomycetes are amoeboid protists primarily found in forest ecosystems. However, their inhabitation and ecology on twig litter remain poorly understood. Therefore, myxomycete species richness and diversity in a forest, canopy tree species and types, and the microenvironmental factors influencing their distribution were assessed. In a natural mid-temperate forest of western Japan, twig litter was seasonally sampled on the forest floor under nine canopy trees selected by different tree types and large, long-lived trees. Using moist chamber cultures (MCs), twigs were incubated to induce myxomycete fruiting. As a result, 60% of the 380 MCs produced fruiting bodies of 33 myxomycete taxa from 21 genera. Ordination of 18 myxomycete communities using non-metric multidimensional scaling distinguished two seasonal groups. The arrangement of the communities was significantly correlated with environmental factors, such as twig pH, soil pH, and diameter at breast height. Large, long-lived trees had characteristically distinct ecological habitats for myxomycetes on twig litter. Members of Cribrariales and Trichiales were dominant on coniferous twigs, whereas Physarales dominated evergreen twigs. This study suggests that canopy trees shape myxomycete communities as a microhabitat in a forest ecosystem, and a mid-temperate forest maintains a high species diversity of myxomycetes, making it an important biodiversity hotspot.