Marine macroalgae harbour abundant and diverse assemblages of epifauna. Patterns of distribution and abundance of epifauna, which are often variable in space and time, differ markedly among macroalgae species. Non-indigenous seaweeds may alter composition and structure of epifaunal assemblages and therefore harbour different assemblages from those associated with native macroalgae. In this study, we analysed the epifaunal assemblages associated with the native algae Bifurcaria bifurcata and the invasive alga Sargassum muticum on the southern part of the Galician coast (north-west Spain). In particular, we tested the hypothesis that there were differences in the epifaunal assemblages associated with the native and invasive algae. We used a hierarchical spatial sampling design to identify if these differences were consistent over space and time. Results indicated that there were significant differences between epifaunal assemblages associated with both algae. The fact that such differences were, in general, consistent at different spatial scales suggests that biological factors related to the specific habitat might play a more important role than physical factors as determinants of epifaunal distribution. This study also showed that S. muticum seems to supply a new and additional habitat for the native epifauna, contributing to increases in the spatial and temporal variability of epifaunal assemblages.