Polygon tundra characterizes large areas of arctic lowlands. The micro-relief pattern within polygons offers differentiated habitats for testate amoeba (testacean)communities. The objective of this study was to relate testacean species distribution within a polygon to the environmental setting. Therefore, testaceans from four cryosol pits dug at different locations within a low-centered polygon were studied in the context of pedological and pedochemical data, while ground temperature and ground moisture were measured over one summer season. The study site is located on the Berelekh River floodplain (Indigirka lowland, East Siberia). The environmental data sets reflect variations along the rim-to-center transect of the polygon and in different horizons of each pit. The testacean species distribution is mainly controlled by the soil moisture regime and pH. Most of the identified testaceans are cosmopolitans; eight species are described from an arctic environment for the first time. Differences in environmental conditions are controlled by the micro-relief of polygon tundra and must be considered in arctic lowland testacean research because they bias species composition and any further (paleo-)ecological interpretation.