Microzonation of testate amoebae and ciliates in relation to physical and chemical parameters in different species of mosses in peatland were studied. Regardless of the species of mosses, similar micro-vertical differentiation of these protozoa was ascertained. A similar number of species, like the abundance, significantly increased in the deepest sampling depth. The upper-most sampling of the mosses (0–5 cm) was dominated by mixotrophic taxons, whereas the deepest sampling level (5–10 cm) shown the increase of the proportion of bacterivore species. In peatlands the factors limiting the occurrence of ciliates and testate amoebae are physio-chemical suitablilty – mainly the total organic carbon content and water table depth, but with somewhat lower levels of pH and species of mosses.