The pervasive effects of invasive ecosystem engineers, that is those species that modify their environment, are well documented, but rarely have the broader impacts of one foundation invertebrate species being replaced by another been examined. In New Zealand, green-lipped mussels, Perna canaliculus, commonly dominate wave-exposed rocky shores. The recent appearance of an invasive ecosystem engineer, the ascidian Pyura doppelgangera, at the very northern tip of New Zealand now threatens to exclude these bivalves from this habitat. Here, we report major shifts in assemblages associated with the invader and chronicle its continued spread. We examined epibiota associated with clumps of mussels and clumps of Pyura from two rocky shore habitats—pools and emergent substrata at two locations. We detected some differences in species richness in biota associated with the two foundation species, but faunal abundance only differed between the locations. These minor changes were dwarfed by the shift in species composition within clumps of each foundation species. Molluscs, particularly gastropods, and crustaceans dominated the assemblage within mussels. In contrast, tubicolous polychaetes dominated the fauna associated with the ascidian. Sessile epifauna, notably barnacles and calcareous tube-dwelling polychaetes, were common on mussels, but never encountered on the ascidian. Multivariate analysis revealed marked dissimilarity (>80%) between the characteristic mussel and ascidian faunas with virtually no overlap. This biotic shift overshadowed any differences between habitats and locations. The broader implications of these faunal shifts for local and regional patterns of biodiversity, as well as ecosystem function, remain unclear, but deserve further attention.