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Changes in the relative abundance of marine megafauna (whales, dolphins, sharks, turtles, manta rays, dugongs) from aerial survey sightings in the waters adjacent to Ningaloo Reef between June 2000 and April 2002 are described. Generalised linear models were used to explore relationships between different trophic guilds of animals (based on animal sighting biomass estimates) and biophysical features of the oceanscape that were likely to indicate foraging habitats (regions of primary/secondary production) including sea surface temperature (SST), SST gradient, chlorophyll-a (Chl-a), bathymetry (BTH) and bathymetry gradient (BTHg). Relative biomass of krill feeders (i.e. minke whales, whale sharks, manta rays) were related to SST, Chl-a and bathymetry (model [AICc] weight = 0.45) and the model combining these variables explained a relatively large amount (32.3%) of the variation in relative biomass. Relative biomass of fish/cephalopod feeders (dolphins, sharks) were weakly correlated with changes in SST, whereas that of other invertebrate/macroalgal feeders (turtles, dugong) was weakly correlated with changes in steepness of the shelf (bathymetry gradient). Our results indicate that biophysical variables describe only a small proportion of the variance in the relative abundance and biomass of marine megafauna at Ningaloo reef.