Despite decades of studies on the differential distribution of polyploid organisms, the causes of this pattern have yet to be elucidated. This study aimed to explore some of the possible physiological mechanisms explaining the differential northern distribution of polyploid clones of Daphnia pulex compared to the one of the diploid parental species. The critical thermal minimum (CTmin) was measured in 17 D. pulex clones of contrasted ploidy (diploid and triploid) and geographic origins (temperate and subarctic climates) reared under low and high temperatures (16 and 24 °C). Triploid clones had better cold tolerance (lower CTmin) than both sympatric and temperate diploid clones. No significant association was found between CTmin and body size nor with cell size. We suggest that triploids might express a cold shock resistant phenotype related to higher gene expression and/or fatty acid profiles. Cold tolerance can be viewed as one of the possible reasons for polyploid preponderance in subarctic climates.