Displacement of native plant species by non-indigenous congeners may affect associated faunal assemblages. In endangered salt marshes of south-east Australia, the non-indigenous rush Juncus acutus is currently displacing the native rush Juncus kraussii, which is a dominant habitat-forming species along the upper border of coastal salt marshes. We sampled insect assemblages on multiple plants of these congeneric rushes in coastal salt marshes in Sydney, New South Wales, Australia, and compared the abundance, richness, diversity, composition and trophic structure between: (i) J. acutus and J. kraussii at invaded locations; and (ii) J. kraussii at locations either invaded or not invaded by J. acutus. Although J. acutus supported a diverse suite of insects, species richness and diversity were significantly greater on the native J. kraussii. Moreover, insect assemblages associated with J. kraussii at sites invaded by J. acutus were significantly different from, and more variable than, those on J. kraussii at non-invaded sites. The trophic structure of the insect assemblages was also different, including the abundance and richness of predators and herbivores, suggesting that J. acutus may be altering consumer interactions, and may be spreading in part because of a reduction in herbivory. This strongly suggests that J. acutus is not playing a functionally similar role to J. kraussii with respect to the plant-associated insect species assemblages. Consequently, at sites where this non-indigenous species successfully displaces the native congener, this may have important ecological consequences for community composition and functioning of these endangered coastal salt marshes.