In Lake Ontario, the diets of slimy sculpin Cottus cognatus and lake whitefish Coregonus clupeaformis shifted from a diet dominated by the burrowing amphipod, Diporeia, and to a lesser extent, Mysis, to a more diverse diet, after Diporeia collapsed, to one dominated by Mysis and prey that were formerly less important or uncommon such as Chironomidae, Oligochaeta, and Ostracoda. Additionally, lake whitefish still preyed on native mollusks like Sphaeriidae and Gastropoda, but also preyed on exotic mollusks, Dreissena spp., which are swallowed intact and subsequently crushed in its muscular stomach. Whether Diporeia was abundant (1992) or scarce (1999), selection indices for Diporeia by slimy sculpins was positive, suggesting that Diporeia was a preferred prey. Unlike lake whitefish, slimy sculpins avoided Dreissena; therefore, energy diverted to Dreissena production was a real loss for slimy sculpins. The shifts in the diet of these benthic fishes corresponded with drastic changes in the benthic community between 1992 and 1999. The collapse of Diporeia, formerly the most abundant macroinvertebrate in the benthic community, along with sharp declines in the abundance of Oligochaeta and Sphaeriidae, coincided with the establishment and rapid expansion of Dreissena bugensis, the quagga mussel, and to a lesser degree Dreissena polymorpha, the zebra mussel. It appears that the Diporeia population first collapsed at depths >70 m in southeastern Lake Ontario by autumn 1992, at shallower depths in the eastern Lake Ontario by 1995, and along the entire south shore line at depths <100 m, and perhaps in some areas >100 m by 1999. In response to the disappearance of Diporeia, populations of two native benthivores, slimy sculpin and lake whitefish, collapsed in eastern Lake Ontario, perhaps due in part to starvation, because Diporeia was their principal prey. Presently, alternative food resources do not appear sufficient to sustain these two benthivores at their former levels of abundance. We do not expect slimy sculpin and lake whitefish to recover unless Diporeia returns to earlier levels of abundance.