Populations often face changes in environmental conditions in a relatively short timescale, which may lead to microevolution of traits to cope with these changing selective pressures. Here, we demonstrate microevolution of a physiological trait in a natural population of the water flea Daphnia magna. Levels of the stress protein Hsp60 showed genetic variation, indicating in situ evolutionary potential, and the levels increased through time. The observed microevolutionary increase did not fit the historically documented changes in fish predation pressure in this pond, but it paralleled an increase in the load of infective stages of epibionts through time. In line with this, the locally most abundant epibiont caused an induction of Hsp60. Because stress proteins show evolutionary potential and protect organisms against a wide array of environmental factors, microevolution of stress proteins in natural populations is likely to be common.