Organisms tend to decrease in size with increasing temperature by phenotypic plasticity (the temperature-size rule; ectotherms) and/or genetically (Bergmann’s rule; all organisms). In this study, the evolutionary response of body size to temperature was examined in the cyclically parthenogenetic rotifer Brachionus plicatilis. Our aim was to investigate whether this species, already known to decrease in size with increasing temperature by phenotypic plasticity, presents a similar pattern at the genetic level. We exposed a multiclonal mixture of B. plicatilis to experimental evolution at low and high temperature and monitored body size weekly. Within a month, we observed a smaller size at higher temperature, as compared to body size at lower temperature. The pattern was consistent for the size of both mature females and eggs; rotifers kept at high temperature evolved to be on average 14% (after 2 weeks) and 3% (after 3 weeks) smaller than the ones kept at low temperature (10 and 5% in the case of eggs, respectively). We therefore found that B. plicatilis is genetically programmed to adjust its body size-to-environmental temperature.