Distribution, ecology and coexistence of cyanobacterial and algal populations have been analysed in a variety of bogs and related microhabitats found in Bohemian Forest, a mountain range with three basic mire types: (i) valley raised-bogs situated at middle altitude, (ii) patterned mires on rainy and cold summit plains, and (iii) young kettle-hole bogs in the lee of glacial cirques. Almost 230 species of blue-greens and algae were identified in the studied mires. Maximum number was found in patterned mires (mean ± s.d.: 99 ± 29 species), lesser abundance in kettle-hole bogs (77.5 ± 13 species), and the least number in the valley raised-bogs (59 ± 8.5 species). Representatives of the Chlorophyceae and Zygnematophyceae were the most common species; the patterned mires were rich also in the Cyanobacteria and Bacillariophyceae; the valley raised-bogs abounded with the Bacillariophyceae. Only about 10 % of the identified species are common components in all bog types studied. Several notable species were collected and identified in these mires: (a) Cyanodictyon turfosum and Ankistrodesmopsis gabretae-silvae is a species newly described for science, (b) Rhabdoderma vermicularis was for the first time identified after its earlier description, (c) Cyanobacteria Eucapsis alpina, Merismopedia angularis, and Rhabdogloea linearis, and the Chlorophytes Monoraphidium tatrae, Elakatothrix parvula became new members of the Czech algal flora. According to ordination by the RDA analysis, composition of the blue-greens and algae differed in the three mire types and in human-disturbed mires. The diversity was significantly correlated to the chemistry of environment (pH and conductivity of water), while the meso-climate (mean annual temperature, annual precipitation, duration of snow-pack) and altitude appeared as insignificant factors. The DCA analyses in valley raised-bogs suggested differentiation of microhabitats according to species composition in less shaded lagg and in Sphagnum-moss carpets. In the patterned mires, aerophytic and plankton communities display a high similarity in species composition, however, the linear responses of species to environmental gradients, evaluated by the PCA analyses, showed the importance of microhabitat variety for the species-richness of individual bogs. The highest number of up to 90 species of cyanobacteria and algae was ascertained in submerged moss carpets and on mud-bottoms.