Synurophytes are planktonic protists whose cells are covered with silica scales. According to the temperature-size rule, protists decrease in size with increasing temperature. Here, we showed that inorganic silica scales responded to increasing temperature in the same way as the cells did. Two species, Mallomonas tonsurata and Synura petersenii, were cultivated at five temperature levels (5, 10, 15, 20 and 25°C) and the methods of geometric morphometrics were applied for scale size and shape data analyses. We observed that the shape of the scales was significantly affected by the cultivation temperature. The overall shape change from rounded, circular scales to oval or more elongated scales seemed to be a general feature in synurophytes and may be considered a consequence of rising temperature. Moreover, the difference in shape remained significant even if the effect of size (allometric effect) was separated. Finally, we compared the level of the scales' morphological variation among all temperature treatments. The results indicated that the cultivation temperature of 25°C negatively affected cellular processes involved in scale biogenesis. The use of the scale shape data has potential in palaeoecological research.