The testate amoebae (Protozoa: Testacealobosea and Testaceafilosea) are a group of free-living protozoans. In 2011, in course of the POLYGON project we investigated the population of testate amoebae in across six polygons in transects from the polygon rim towards the center. At each point, samples were taken from different soil horizons of the active layer. Furthermore, we studied testate amoebae communities in sediments of polygon ponds. In total, 126 samples were analyzed. The study aims at the analysis of environmental and spatial distribution patterns of testate amoebae in a polygonal tundra landscape. The study area was located in the floodplain and the adjacent thermokarst-affected lowland along the Berelekh River, a tributary of the Indigirka River, 28 km northwest of the settlement of Chokurdakh near the Kytalyk WWF (World Wildlife Fund) station (70° 83' 12.1'' N; 147° 48' 29.9'' E). The testate amoebae records obtained consist of 150 taxa at the species and intraspecific levels related to 25 genera. The number of taxa per sample varies from individual finds the permafrost table to 20 or more species and subspecies in the surface horizons. The following conclusions can be drawn: (1) Environmental parameters that affect testate amoeba communities in arctic polygon tundra vary within the studied polygon from the rim toward the center and/or with depth; (2) the most important controls on testacean species distribution are the moisture regime, which varied according to position within the studied polygon, and pH; (3) the number of species increases from the polygon rim toward the center where warmer and wetter conditions prevail in a seasonally deeper thawed active layer; (4) along the rim-to-center gradient soil-eurybiontics and xerophiles are replaced by sphagnophiles in surface samples, and soil-eurybiontic species are replaced by hygro-hydrophiles in lower Oi and Oe soil horizons; (5) using the ecological indication of testacean taxa, increasing soil moisture can be only observed for the Oi and Oe horizons; and (6) lowermost (and coldest) Bg horizons directly above the permafrost table lack testaceans. In comparison to the modern testate amoebae record described above, 212 taxa have been found in late Pleistocene and Holocene sediments of polygon origin at various sites of NE Siberia. Differences in the paleoclimatic setting and corresponding soil conditions are reflected by species diversity and ecological indication of testate amoebae taxa. At least temperature variations during the Quaternary past can be distinguished by the composition of fossil testate amoebae communities. The study was conducted under the auspices of the joint Russian–German project 'Polygons in tundra wetlands: State and dynamics under climate variability in polar regions' (RFBR grant no. 11-04-91332-NNIO-a, grant no. HE 3622-16-1). Financial support came also from the RFBR Project no. 11-04-01171-a 'Geography and ecology of soil-inhabiting testate amoebae'.