Among various seagrass ecosystem services, one of the most important one is provisioning services that support various plants and animals. In seagrass beds, epifaunal communities (assemblages of small invertebrates) play a key role in trophic cascades and have strong associations with bed-forming seagrass species. Introduced species are increasing worldwide, and bed-forming introduced seagrasses are establishing in new regions, including Zostera japonica (ZJ) from Japan (native) to Canada (introduced). In their introduced region, epifaunal associations with ZJ are occasionally studied and compared with the native congener, Z. marina (ZM). However, these results have not been compared within their native region. In this study, we aim to compare epifaunal communities associated with ZJ and ZM, and how the epifaunal communities differ between Japan, where both species are native, and Canada, where ZJ is introduced. We collected seagrass and epifauna from multiple sites in both regions and compared trends in community composition and diversity indices. Results suggested that ZJ community composition was significantly different from ZM, in both Japan and Canada. However epifaunal diversity indices were only significantly different in Canada, where ZJ had a less diverse community than ZM. These regional comparison results will provide fundamental scientific knowledge required for environmental management.