Folsomia manolachei Bagnall, 1939 (Collembola), is a widespread and common European species. However, it may represent a complex of species also associated with the climatically more extreme environments of the karst landforms. Three species of the genus Folsomia, distributed in the Slovak Karst region (Central Europe), namely three different populations of F. manolachei, and one population of F. penicula and F. candida, were analysed using a partial sequence of the mitochondrial cytochrome c oxidase subunit I (COI barcoding section). The DNA barcoding suggested the existence of cryptic diversity in populations of the eurytopic species Folsomia manolachei. The cold‐adapted population of ‘F. manolachei’ was abundant in primary soil on stony debris near the permanent floor ice (yearly air temperature ~0°C) in the collapsed karst doline of the Silická ľadnica Ice Cave. It showed a genetic differentiation supported by intra‐ and interspecific distances that ranged from 0.0% to 1.4% and from 19.2% to 24.0%, respectively. Analysis using Taxon DNA showed a large barcoding gap between intra‐ and interspecific COI sequences. Genetic differentiation suggests a scenario of cryptic speciation in the population of ‘F. manolachei’ occupying harsh soils near the floor ice. A survival test showed the different responses of ‘F. manolachei’ and other populations to low temperature. Within a temperature range from −3 to −10°C, the ‘F. manolachei’ population from Silická ľadnica was the most cold‐resistant, showing a lethal dose LD50 of −7.8°C. The two forest populations of F. manolachei had LD50 −6.1°C and −6.0°C, respectively; the most cold‐sensitive F. penicula showed an LD50 of −5.4°C. The survival of the tested springtails significantly decreased with temperature (p < 0.0001). The lethal temperature and the shape of the survival–temperature curves were different in different populations. The impact of population was significant at p < 0.0001, and the interaction between population and temperature at p < 0.039 was significant as well. Crypticity vs. phenotypic plasticity in Folsomia manolachei populations is discussed in terms of DNA barcoding and the cold tolerance data provided by this study.