The silica-scaled chrysophytes (Synurophyceae and Chrysophyceae) are a small group of freshwater flagellates with cells enclosed within a morphologically species-specific scale case. Thirty taxa were found during an investigation of peaty pools in the National Nature Monument Swamp and the plankton of Brehynsky Pond, Czech Republic. Along with cosmopolitan and widely distributed species, Mallomonas adamas and M. maculata, which shows a patchy geographic distribution, and M. clavus, Synura lapponica and Chrysosphaerella longispina, which show a northern temperate distribution, were found. Mallomonas annulata, M. heterospina, M. paludosa, M. papillosa, M. calceolus, M. pumilio, Synura echinulata, S. lapponica and Chrysosphaerella longispina belong to a group of cool-water taxa. Mallomonas multisetigera, M. ouradion, M. papillosa, Synura echinulata, S. sphagnicola and Paraphysomonas vestita have an ability to form dominant populations in extremely acidic environments (pH 3.5-4.0). The species Mallomonas clavus, M. favosa, M. maculata, M. rasilis and Chrysosphaerella longispina are recorded here for the first time from the Czech Republic.