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Temperature is a ubiquitous environmental factor affecting physiological processes of ectotherms. Due to the effects of climate change on global air and water temperatures, predicting the impacts of changes in environmental thermal conditions on ecosystems is becoming increasingly important. This is especially crucial for migratory fish, such as the ecologically and economically vital salmonids, because their complex life histories make them particularly vulnerable. Here, we addressed the question whether temperature affects the morphology of brown trout, Salmo trutta L. spermatozoa. The fertilising ability of spermatozoa is commonly attributed to their morphological dimensions, thus implying direct impacts on the reproductive success of the male producing the cells. We show that absolute lengths of spermatozoa are not affected by temperature, but spermatozoa from warm acclimated S. trutta males have longer flagella relative to their head size compared to their cold acclimated counterparts. This did not directly affect sperm swimming speed, although spermatozoa from warm acclimated males may have experienced a hydrodynamic advantage at warmer temperatures, as suggested by our calculations of drag based on head size and sperm swimming speed. The results presented here highlight the importance of increasing our knowledge of the effects of temperature on all aspects of salmonid reproduction in order to secure their continued abundance.