Invasive plants that displace native floral communities can cause changes to associated invertebrate species assemblages. Using a mini-review of the literature and our own data we add to the still considerable debate about the most effective methods for testing community-level impacts by invasive species. In endangered saltmarshes of southeast Australia, the non-native rush Juncus acutus L. is displacing its native congener J. kraussii Hochst., with concurrent changes to floral and faunal assemblages. In two coastal saltmarshes, we tested the hypothesis that the ability to detect differences in the invertebrate assemblage associated with these congeneric rushes depends on the microhabitat of the plant sampled. We used three sampling methods, each targeting specific microhabitats: sweep netting of the plant stems, vacuum sampling of the plant tussock, and vacuum sampling of the ground directly below the plants. Over 3800 individuals and 92 morphospecies were collected across four main taxa: gastropods, crustaceans, hexapods and arachnids. Detection of differences in invertebrate density, richness and composition associated with native compared with non-native rushes was dependent on the microhabitat sampled and these differences were spatially variable. For example, at one saltmarsh the stems and tussock of J. acutus had a lower density and richness of total invertebrates and hexapods than those of the native J. kraussii. In contrast, crustaceans on the ground were in greater abundance below J. acutus than J. kraussii. This study demonstrates that on occasions where overall differences in the assemblage are not detected between species, differences may become apparent when targeting different microhabitats of the plant. In addition, separately targeting multiple microhabitats likely leads to a greater probability of detecting impacts of invasion. Comparing the invertebrate assemblage without differentiating between or sampling an array of microhabitats can fail to determine the impact of invasive species. These results highlight that a combination of methods targeting different microhabitats is important for detecting differences within the invertebrate community, even for phylogenetically related species.