Differences in the carbohydrate composition were revealed among spores of fungi belonging to Zygomycetes, Ascomycota, Basidiomycota, and Oomycota, part of the novel kingdom Chromista. It was shown for the first time that Phytophthora infestans contains arabitol in addition to glucose and trehalose. Sucrose was detected in Pleurotus ostreatus basidiospores. It was established that Blakeslea trispora stylospores contain inositol. The dependence of the spore carbohydrate composition on the temperature of the habitat of the corresponding species is discussed. It was shown that the cytosol of the conidia is dominated by trehalose and inositol under hypothermic conditions and by mannitol and glucose under hyperthermic conditions. Neomycota and Eomycota were shown to differ in their responses to stress (starvation), which correlated with the differences in the carbohydrate composition of the spore cytosols. Assuming that cytosol carbohydrates perform a protective function, we explain the higher viability of conidia compared to stylo- and sporangiospores.