The composition and structure of epifaunal assemblages associated with the non-native Gracilaria vermiculophylla (Rhodophyta) was analyzed and compared to those associated with the native Ulva rigida (Chlorophyta). In a shallow coastal lagoon of the northwestern Adriatic Sea, we collected samples of each species from two different sites for a five-year period. Epifaunal assemblages differed according to the habitat attributes provided by each type of seaweed. Amphipods comprised most of the epifanual abundance on U. rigida, while Gastropods on G. vermiculophylla. The architecturally more complex G. vermiculophylla supported higher species richness and diversity of associated macrofauna. Differences in structural complexity of the two seaweeds (irregularly branched vs flat sheet-like thalli) allow different (taxonomically and functionally) epifaunal assemblages.