This study examined the relationship between clonal dynamics and population stability of natural Daphnia pulex populations experiencing seasonal environmental variation. It shows that the degree of asynchrony in a population's clonal dynamics is tightly linked to its population-level stability. Populations whose clonal abundances were more asynchronous were more stable temporally. Variation in asynchrony was related to variability in primary productivity, and experiments using clones from the study populations revealed significant genotype by environment interactions in response to food level.