Western Carpathian spring fens (groundwater-fed wetlands characterized by specific vegetation) represent a rare and unique biotope whose aquatic insects have not been studied in detail up to now. Therefore, the aims of this study were to describe the stonefly larvae assemblages (identified into the species level based on recording imagines) and to isolate the main environmental factors controlling species composition. The study was carried out in 2006 at 11 sites in the borderland between the Czech Republic and Slovakia. Stonefly adults were sampled using a Malaise trap placed in the centre of each fen. In total 1,691 specimens of 33 species were found. This species richness was quite surprising particularly when taking into account small size and isolation of these sites. A cluster analysis of samples separated the studied fens into three groups representing three types of spring fens: the calcareous fens with strong tufa precipitation, the brown-moss rich fens, and the spring meadows. This classification reflected the arrangement of samples along the second ordination axis (detrended correspondence analysis) whereas the first ordination axis displayed the variability of stonefly taxocoene during the year. According to results of canonical correspondence analysis (CCA), the structure of stonefly taxocoene was influenced by the season and substrate characteristics of studied fens.