Marine reserves are used widely throughout the world to conserve biodiversity, but in many instances uncertainties exist over how well these areas represent biodiversity at a regional scale (i.e. 100–1000 km). In the present study, infaunal assemblages were examined in the eastern Great Australian Bight (GAB) to evaluate the efficacy of the Benthic Protection Zone of the GAB Marine Park in representing regional biodiversity. Distributional patterns in infauna were further examined in relation to epifaunal species composition and environmental conditions to investigate structural forcing. Grab samples of infauna were collected from the same 65 sites sampled in an earlier survey of epifauna. In total, 240 taxa belonging to 11 phyla were collected. Most taxa were uncommon, with 96% representing less than 2% of the total number of individuals collected and 39% occurring at only one site. Unlike the epifauna, the infauna of the eastern GAB does not appear to be particularly diverse. Sessile filter feeders dominated the infaunal communities of the inner shelf, whereas motile, deposit-feeding organisms dominated the shelf break. As was the case with the epifauna, the highest numbers of taxa and individuals were recorded near the head of the bight and in inner-shelf waters off the western Eyre Peninsula, where productivity is enhanced by upwelling. Cluster analysis identified three community groupings, which were strongly correlated with depth. All three communities and 72% (172) of the 240 taxa collected were represented within the Benthic Protection Zone of the GAB Marine Park, confirming findings from the epifaunal survey that this protected area is well placed to represent the benthic biodiversity of the eastern GAB.