The objective of the study was to investigate the taxonomic structure and spatial distribution of ciliate communities, and to identify the environmental factors determining the taxonomic structure of the assemblages. Additionally, we compared ciliate communities inhabiting ponds on King George Island (Antarctica) with those on other islands of the maritime Antarctic. The taxonomic richness, abundance and biomass of ciliates in microbial mats varied among ponds increasing with their eutrophication level. As the level of eutrophication increased, there was a decrease in the abundance of predatory and omnivorous ciliates and a decrease in that of algivorous taxa. The canonical correspondence analyses of the spatial distribution of ciliates showed that all environmental variables together explained 76% of the total variance. The Monte Carlo permutation test showed that dissolved orthophosphates, nitrate and total organic carbon had the most significant effect on the distribution of ciliates. The proportions of individual functional groups of ciliates varied among ponds. The proportion of heterotrophic taxa increased with the trophic state of the ponds, while the proportion of mixotrophic taxa decreased.