A combination of founder effects and local adaptation – the Monopolization hypothesis – has been proposed to reconcile the strong population differentiation of zooplankton dwelling in ponds and lakes and their high dispersal abilities. The role genetic drift plays in genetic differentiation of zooplankton is well documented, but the impact of natural selection has received less attention. Here, we compare differentiation in neutral genetic markers (FST) and in quantitative traits (QST) in six natural populations of the rotifer Brachionus plicatilis to assess the importance of natural selection in explaining genetic differentiation of life-history traits. Five life-history traits were measured in four temperature × salinity combinations in common-garden experiments. Population differentiation for neutral genetic markers – 11 microsatellite loci – was very high (FST = 0.482). Differentiation in life-history traits was higher in traits related to sexual reproduction than in those related to asexual reproduction. QST values for diapausing egg production (a trait related to sexual reproduction) were higher than their corresponding FST in some pairs of populations. Our results indicate the importance of divergent natural selection in these populations and suggest local adaptation to the unpredictability of B. plicatilis habitats.