Microscopic epibionts are important components of an intertidal ecosystem. However, because the epibionts are established on habitats provided by basibiont (host) organisms, the epibionts are affected by both the characteristics of basibionts and the environmental conditions on the shore. Here, we hypothesized that variations in the epibiont community were affected by the mobility, size, and surface roughness of the basibiont organisms, and environmental conditions during a one-month period in spring. Epibionts growing on 16 basibiont species belonging to Gastropoda, Bivalvia, Polyplacophora and Echinoidea, as well as those that had settled on plastic objects were collected from a rocky shore in Niigata, Japan. Most epibionts collected were diatoms, and the highest epibiont density was recorded on the surfaces of the limpet Cellana toreuma. The epibiont community changed significantly from April to May, and was also shaped by the characteristics of the basibionts. The results indicated that basibionts with sessile, large, or smooth surfaces had higher taxonomic richness, Simpson diversity, and epibiont density than those with mobile, small, or rough surfaces. Multivariate analysis of the epibiont community confirmed the importance of these basibiont characteristics and the survey month. Six groups of epibiont community were identified based on their contrasting sample communities, and each had their own indicator species. The results indicate that both environmental changes from April to May and changes in basibiont species promote changes in the epibiont community in this coastal region.