Diatoms are among the most important primary producers in alpine and polar freshwaters. Although temperate diatoms are sensitive to freezing, polar diatoms often exhibit more resistance. This is particularly true for members of the (predominantly terrestrial) Pinnularia borealis species complex. However, it remains unclear to what extent this resistance applies to other representatives of the genus. Here, we compare the freezing‐stress tolerance of 11 freshwater, benthic strains representing different species of Pinnularia (including Caloneis) from polar, alpine, and temperate habitats. As vegetative cells, strains were exposed to freezing temperatures of −4, −10, −20, −40, −80, and −196°C. Survival was assessed by light microscopy and photosynthetic measurements. We observed vegetative cells to be sensitive to low freezing temperatures; only “mild” freezing was survived by all tested strains, and most tested strains did not survive treatments ≤−10°C. However, individual strain sensitivities appeared related to their original habitats. For example, polar and alpine strains better withstood “mild” and “moderate” freezing (−4 and −10°C, respectively); although temperate strains were significantly affected by the “mild” freezing treatment, polar and alpine strains were not. The −10°C treatment was survived exclusively by polar strains, and only P. catenaborealis survived all treatments. Interestingly, this species exhibited the lowest survival in the −10°C treatment, potentially implying some metabolic activity even at freezing temperatures. Thus, despite more extensive sampling throughout the genus and finer temperature scaling compared to previous studies, the remarkable freezing‐stress tolerance of the P. borealis species complex remains unique within the genus.