There are hardly any data concerning the vertical micro−distribution of protozoa in water column in cryoconite holes on the glacier surface. Such comparisons can provide insights into the ecology of protozoa. The present research was made on Ecology Glacier (South Shetland Islands, Antarctic); vertical microzonation of c iliates in relation to physical and chemical parameters in cryoconite holes was studied. The density and biomass of protozoans significantly differed between the studied stations (cryoconite holes), with the lowest numbers in the surface water and the highest in the bottom water. The surface waters were dominated by mixotrophic and omnivorous taxa, whe reas the deepest sampling level has shown the increase of the proportion of bacterivore species . Ordination analysis indicated that TN and P−PO 4 can strongly regulate the abundance and species composition of protozoa. The redundancy analyses (RDA) showed that the ciliate communities can be separated into two groups. The first group included species associated with surface water: Halteria grandinella and Codonella sp. The second group included species that are associated with bottom water: Prorodon sp. , Holosticha pullaster , Stylonychia mytilus −complex and small scuticociliates.