A field and laboratory study was carried out over 3 yr to determine relationships between seasonal and interannual changes in temperature (year-specific temperature courses, presence or absence of ice in winter) and the genetic structure (composition of multilocus genotypes [MLGs]) of a Daphnia longispina assemblage. Field studies on temperature and genetic structures were linked with laboratory analyses to evaluate the thermal tolerance of long-term 12uC-, 18uC-, and 24uC-acclimated clonal lineages (CLs) derived from abundant MLGs sampled in the field (surface water and thermocline). The tolerance to warm temperatures (heat tolerance) was lowest in CLs derived from MLGs that were dominant directly after or before winter (winter-CLs), higher in ''spring-autumn-CLs,'' and highest in ''summer-CLs.'' Winter-CLs also showed the highest degree of physiological plasticity. The differences in heat tolerance were mainly related to the different genotypes of the phosphoglucomutase (PGM) locus. Temperature conditions during winter and early spring affected the heat tolerance of all CLs as well as the success of different winter survival strategies (overwintering, resting eggs). Heat tolerance was lowest in CLs derived from MLGs sampled in 2006 (after the coldest winter and spring period), higher in CLs from 2005 (after a less cold winter and spring period), and highest in CLs from 2007 (after a warm, ice-free winter). In addition to other environmental factors (predation, parasitism, food), seasonal and interannual changes in temperature affect Daphnia genetic structure through genetic differences in thermal responses, thermal tolerance, and physiological plasticity.Depending on environmental conditions, daphnids alter between asexual (parthenogenesis) and sexual reproduction. Parthenogenetic reproduction, which occurs under favorable conditions (often from spring until autumn in temperate zones), results in the propagation of a varying number of coexisting genotypes (clonal population structure) (Hebert and Crease 1980;Weider 1985; Pantel et al. 2011) that originated from sexual reproduction. Sexual reproduction is inducible by unfavorable conditions (often in late autumn in temperate zones). Thus, selection acting on the different clones, which alters the clonal population structure, as well as genetic recombination and the recruitment of sexually derived genotypes, which arise from resting eggs, are essential factors for the maintenance of genetic diversity in Daphnia populations (Hembre and Megard 2006). Several studies have reported on selection by the spatiotemporal heterogeneity of the environment including predation (De Meester et al. 1995;Cousyn et al. 2001), parasitism (Mitchell et al. 2004), and food quality (Weider et al. 2005; Brzeziński et al. 2010). The influence of spatiotemporal changes in water temperature on the genetic structure of Daphnia populations has also been studied. Carvalho (1987), for instance, reported for Daphnia magna a higher viability and fecundity of winter clones in cold water...