• Australia;
  • diversity;
  • macroecology;
  • reef fish assemblages;
  • spatial patterns;
  • variability

In this study, fishes and habitat attributes were quantified, four times over 1 year, on three reefs within four regions encompassing a c. 6° latitudinal gradient across south-western Australia. The variability observed was partitioned at these spatio-temporal scales in relation to reef fish variables and the influence of environmental drivers quantified at local scales, i.e. at the scale of reefs (the number of small and large topographic elements, the cover of kelp, fucalean and red algae, depth and wave exposure) and at the scale of regions (mean and maximum nutrient concentrations and mean seawater temperature) with regard to the total abundance, species density, species diversity and the multivariate structure of reef fishes. Variation in reef fish species density and diversity was significant at the regional scale, whereas variation in the total abundance and assemblage structure of fishes was also significant at local scales. Spatial variation was greater than temporal variation in all cases. A systematic and gradual species turnover in assemblage structure was observed between adjacent regions across the latitudinal gradient. The cover of red algae within larger patches of brown macroalgae (a biological attribute of the reef) and the number of large topographic elements (a structural attribute of the reef) were correlated with variation observed at local scales, while seawater temperature correlated with variation at the scale of regions. In conclusion, conservation efforts on reef fishes need to incorporate processes operating at regional scales with processes that shape local reef fish communities at local scales.