AbstractZygnematophyceae, a class of freshwater green algae, exhibit distinctive seasonal dynamics. The increasing frequency of cold snaps during the growing season might challenge the persistence of some populations. The present study explored the frost hardiness of two Mougeotia species isolated from different elevations and habitats. Additionally, a phylogenetic (rbcL sequence), ultrastructural and physiological characterization was performed. Both species, grown under standard culture conditions and cold acclimated cultures (+4°C), were exposed to freezing temperatures down to −9°C. Furthermore, ultrastructural‐, hydrogen peroxide (H2O2)‐ and photosynthetic pigment analysis were performed on cells exposed to −2°C, with and without induced ice nucleation. The alpine M. disjuncta showed a higher frost hardiness (LT50 = −5.8°C), whereas the lowland M. scalaris was susceptible to ice. However, frost hardiness did not improve after cold acclimation in either species but rather decreased significantly in M. disjuncta (LT50 = −4.7°C). Despite darkness, prolonged sub‐zero temperatures or freezing induced the activation of the xanthophyll (VAZ) cycle in M. scalaris. Our results demonstrate that frost hardiness varies within the genus Mougeotia and that the VAZ cycle can be activated in the dark under subzero temperature‐ and freezing stress but does not necessarily increase frost hardiness. As highly frost hardy cell types are usually formed at the end of the growing season, the ability of young cells to survive ice formation in the upper subzero temperature range represents a crucial survival strategy in populations exposed to late spring frosts.