Populations of animals and plants often undergo conspicuous ecological changes when subjected to climatic extremes. Evolutionary changes may accompany them but are less easily detected. We show that Darwin's finches on a Galapagos island underwent two evolutionary changes after a severe El Nino event caused changes in their food supply. Small beak sizes were selectively favoured in one granivorous species when large seeds became scarce. The effects of selection were transmitted to the next generation as a result of high trait heritabilities. Hybridization between this species and two others resulted in gene exchange, but only after the El Nino when hybrid fitness was much enhanced under the altered feeding conditions. These observations imply that if global warming increases the frequency or severity of El Nino events on the Galapagos, microevolutionary changes in animal and plant populations are to be anticipated.