El Niño-Southern Oscillation (ENSO) is a global climate variablility, which fundamentally influences environmental patterns of the Humboldt Current System (HCS) off Chile and Peru. The surf clams Donax obesulus and Mesodesma donacium are dominant and highly productive bivalves of exposed sandy beaches of the HCS. Existing knowledge indicates that El Niño (EN, warm phase of ENSO) and La Niña (LN, cold phase of ENSO) affect populations of both species in a different way, although understanding of the mechanisms underlying these effects is still lacking. The aim of this study was to test hypotheses attempting to explain field observations on the effect of strong EN or LN events by using controlled experimental conditions. Growth and mortality rates of both species were registered during a four-week experiment under EN temperature conditions, normal temperature conditions and LN temperature conditions. While D. obesulus exhibited reduced growth and higher mortality under LN conditions, M. donacium showed reduced growth and higher mortality under EN conditions. The results clearly indicate different temperature tolerance windows for each species, possibly reflecting the evolutionary origins of the Donacidae and Mesodesmatidae in regions with contrasting temperature regimes. These results provide experimental support for previous hypotheses suggesting that thermal tolerance is the driving factor behind observed changes in the species distributions of D. obesulus and M. donacium during the extreme phases of ENSO. © 2010 Elsevier Ltd.