Artificial laminated cyanobacterial mats, originating from the bottom sediments of Nivå Bay (The Sound, Denmark), were initiated in 1996–97. The benthic fauna were removed by overnight freezing at -20°C. The diversity of amoebae in intact Nivå Bay sediments and in the artificial mats was compared some four years later. Twenty-nine species of amoebae were recorded from the bottom sediments of the Nivå Bay, and of these, eleven species were found in the artificial mats. Experiments indicated that Vannella simplex, Vannella arabica, Clydonella rosienfieldi and Vannella ebro survived freezing for 36h at-20°C. These results highlight the tolerance of some amoebae to adverse conditions, and support ideas about a “hidden” diversity of amoebae in natural habitats.