Tropical rainforest canopies are renowned for their high invertebrate diversity and abundance. The canopy comprises a range of microhabitats representing very different food resources (including photosynthetic, reproductive, and structural tissues). As these resources vary considerably in temporal and spatial availability, nutritional quality, chemical protection and other attributes, we hypothesized that microhabitats support structurally different invertebrate communities. To test this we used the Australian Canopy Crane to sample invertebrates from mature leaves, flush leaves, flowers, fruit and suspended dead wood from 23 plant species. Invertebrate faunas on different microhabitats varied in taxonomic composition and feeding guild structure in support of the microhabitat differentiation hypothesis. Herbivores were found predominantly on new leaves (Hemiptera, Lepidoptera) and especially flowers (Coleoptera, Thysanoptera), but were relatively uncommon on mature leaves. Instead, the mature foliage community was dominated by predators, especially spiders and ants, and supported high abundances of saprophages. Ripe fruit and dead wood were scarce canopy resources that were utilized by a relatively small number of invertebrates, mostly saprophages and fungivores. Flowers supported a more heterogeneous fauna than the leaves in terms of proportional abundances of taxonomic groups and feeding guilds, both within tree species (evenness) and between tree species (non-uniformity). These results demonstrate microhabitat differentiation in a rainforest canopy and are the first to quantify differences in taxonomic composition, guild structure and abundance patterns between such diverse invertebrate assemblages within host trees. We conclude that studies based only on sampling one microhabitat, and leaves in particular, may provide a distorted picture of invertebrate community structure.