Climate change is expected to result in smaller fish size, but the influence of fishing has made it difficult to substantiate the theorized link between size and ocean warming and deoxygenation. We reconstructed the fish community and oceanographic conditions of the most recent global warm period (last interglacial; 130 to 116 thousand years before present) by using sediments from the northern Humboldt Current system off the coast of Peru, a hotspot of small pelagic fish productivity. In contrast to the present-day anchovy-dominated state, the last interglacial was characterized by considerably smaller (mesopelagic and goby-like) fishes and very low anchovy abundance. These small fish species are more difficult to harvest and are less palatable than anchovies, indicating that our rapidly warming world poses a threat to the global fish supply.