Liparis loeselii (L.) Rich. is an endangered orchid species which occurs in wetland habitats. For successful conservation of this orchid it is necessary to recognize its adaptive traits and special habitat requirements. Therefore, we examined morphological and anatomical traits in relation to the water level, cover of vascular plants and seed viability of L. loeselii in habitats with different water level fluctuations. Field studies of L. loeselii were carried out in nine localities and four habitat types: alkaline fen, calcareous fen with Cladium mariscus, transition mire and quaking bog. The fluctuations of seasonal water level were defined in the range from dry substrate to short time flooding (up to two weeks). Leaf length and width of 30 flowering specimens of L. loeselii as well as angle between the leaf blade and the axis of the inflorescence were measured at each locality. Seed viability and root anatomy were examined in the laboratory. The leaf angle was significantly affected (P < 0.05) by water level in the studied habitat. The leaf length to width ratio in each population of L. loeselii did not show significant differences between the years, but was characteristic for the habitat type. L. loeselii sensitivity to the long-term flooding in the habitat is associated with a lack of aerenchyma in its roots. During short-term flooding specimens of L. loeselii can survive due to a shallow root system and hyponastic leaf movements. As evidenced by seed viability, the most favourable growth conditions for L. loeselii are in the habitats with partially water saturated substrate with balanced water supply.