Macrobenthic community structure in the Fitzroy River estuary was examined from quantitative grab samples collected at 74 depth-stratified stations during 2001. Analysis of variance showed a significant (p<0.05) decline in total abundance from the upper to the lower reaches of the estuary, and a pronounced increase in abundance with depth. Much of this change could be attributed to the distribution of the mat-forming mussel Amygdalum cf. glaberrima, which occurs exclusively in the upper Fitzroy, and in some locations at densities >2000/m2. Spatial gradients in species richness were less compelling, although marked declines in this parameter were evident from the upper to the lower reaches of the estuary. Two infaunal community groupings, corresponding with stations from the upper and lower reaches of the Fitzroy were also identified in ordinations of species abundance data. Neither ordination grouping displayed strong underlying patterns of changing community structure with depth, however distinct shifts in trophic structure were identified. Infaunal communities in the subtidal were dominated by filter feeding organisms (~80% of the total species abundance), while those from the intertidal zone were dominated by deposit feeding polychaete worms. A small proportion of the organisms collected during the survey (7 of 49 species) have never been recorded in the contiguous estuarine waters of Port Curtis, and none of these could be confidently matched with archived Australian material. Whether these species represent un-described endemic organisms or exotic introductions remains to be determined, together with the principal factors underpinning the geographical disparity in species representation.