Six vital strains of amoebae belonging to the genus Flamella (Amoebozoa, Variosea) were isolated from permafrost sediments sampled in Russian Arctic region. Two of them are from late Pleistocene permafrost in North-East of Siberia, and four - from Holocene and late Pleistocene in North-West of Siberia. Light- and electron-microscopic study and molecular phylogeny show that these isolates represent two new species belonging to the genus Flamella. Both species are cyst-forming. This is a remarkable case of high resistance of protozoan cysts, allowing them to survive and recover amoebae population after a very long, geologically significant period of rest; a “snapshot” of evolution in time. This study directly shows for the first time that amoeba cysts can be conserved not only for years and decades but for many thousands years and then recover, contributing to the formation of active microbial community. We propose to name new species as Flamella pleistocenica n.sp. and Flamella beringiania n.sp. Phylogenetic a