Non-indigenous invaders may play ecologically similar roles to native species, and this may be reflected in the abundance, richness and composition of associated species assemblages. We investigated whether associations of epifauna with their macroalgal hosts differed between the non-indigenous Codium fragile ssp. fragile and native, congeneric C. fragile on three rocky shores in southeast Australia. Of the 38 taxa we recorded, 13 were unique to the native Codium and four to non-indigenous individuals. Holdfasts of non-indigenous Codium had double the taxon richness of epifauna compared to native holdfasts, and epifaunal abundances showed a similar but non-significant difference. Patterns of abundance and richness of epifaunal taxa on thalli of native and non-indigenous Codium varied depending on whether these measures were expressed per individual alga, thallus area or number of branches. The composition of epifaunal assemblages between native and non-indigenous Codium were significantly different, but differences among rocky shores were as great as those between macroalgal species. On all shores, two taxa, the gastropod Alaba opiniosa and gammarid amphipods, contributed most to compositional differences between native and non-indigenous Codium, and their abundances were influenced by branch number and associated epiphyte load. Host choice experiments manipulating the complexity and subspecies of Codium revealed that amphipods were more strongly influenced by branch number adjusted for epiphyte load than the identity of Codium. Our results highlight the importance of habitat features, such as structural complexity and associated epiphyte load, in determining whether native and non-indigenous species provide functionally equivalent habitats for associated assemblages.