Using a 9-yr data set, we investigated annual fluctuations in the diet of an apex predator, the Australian fur seal Arctocephalus pusillus doriferus. At Seal Rocks (northern Bass Strait), home to 25% of the entire species population, we assessed diet through collections (1997 to 2006) of scat and regurgitate samples. We identified prey remains of 42 fish taxa and 7 cephalopod taxa. Only crustaceans that were fish parasites or fish prey (amphipods and isopods) were found; no birds were identified in the samples. Six species represented 80% (as frequency of occurrence) of the fish prey, and the arrow squid Nototodarus gouldi represented 70% of cephalopod prey. There was significant annual variability in the diet. Principal component analysis indicated this was variability due to the presence of redbait Emmelichthys nitidus in some years, and its near absence and replacement in other years by increased proportions of barracouta Thyrsites atun, red cod Pseudophycis bachus and leatherjackets (Family Triglidae). Generalised Linear Models indicated the annual variation was related to mean sea surface temperatures in western Bass Strait where the seals foraged. Redbait proliferated in cooler years and were less abundant in warmer years. No corresponding annual correlation was evident between the prey assemblages and either annual fisheries catch-per-unit-effort or the annual mean Southern Oscillation Index. The propensity for diet regimes to persist for several years, then change suggests that oceanographic fluctuations probably influence previously unrecognised multi-year cyclic fluctuations of prey and of Bass Strait ecosystems. © Inter-Research 2008.