This paper is a contribution to the Latitudinal Gradient Project. It describes macro and epifaunal assemblages and habitats at three shallow water locations at the southern end of the western Ross Sea coast, and investigates relationships between faunal composition and environmental characteristics. Many variables (e.g. substrate type, sediment composition, depth, latitude, longitude) contributed to explaining the differences in community composition between locations, with latitude (a likely surrogate for broader scale factors, e.g. ice cover) one of the most important. The percentage explained by environmental characteristics was strongly scale dependent, decreasing with increasing scale of observation. As much as 66% and 75% of the variability in macrofaunal and epifaunal assemblages, respectively, was explained at the smallest scale (i.e. between transects within a location), compared to 9–18% and 11–32%, respectively, at the scale of the entire study. This relationship was also true for species richness and total abundance. This suggests that while small-scale habitat variability will not confound our ability to detect latitudinal gradients in future studies, adequately quantifying the environmental factors important in structuring these communities at larger (latitudinal) spatial scales will be important. Finally, large differences in habitat structure did not translate into large differences in the diversity of fauna, illustrating the difficulty of predicting faunal composition in the Ross Sea based on seafloor topography alone.