Habitat affinities of the red-listed and EU Habitat Directive moss species Hamatocaulis vernicosus and the more widely distributed allied species Scorpidium cossonii and Warnstorfia exannulata were analysed. Ecological preferences of these fen mosses, with respect to water pH, water conductivity, Ellenberg’s moisture and nutrient indicator values, were compared in three different European locations (Bohemian Massif, the West Carpathians and Bulgaria) using logistic regressions fitted by means of Huisman-Olff-Fresco models. Inter-specific co-occurrences of the species were also investigated. Warnstorfia exannulata preferred slightly acid conditions, about pH 5.6 at all the locations studied. Ecological behaviour of S. cossonii was very similar at all the locations, where it occupied base-rich habitats (pH > 7). The pH optimum of H. vernicosus, occupying habitats in the middle part of the base richness gradient, varied between locations from 6.0 in Bulgaria to 6.7–7.0 in the West Carpathians and Bohemian Massif. Niche diversification followed the gradient in Ellenberg nutrient indicator values and was similar at all the locations. In the Bohemian Massif and Bulgaria, the occurrence of W. exannulata was further associated with a relatively high moisture indicated by the Ellenberg indicator value. The results obtained from the Huisman-Olff-Fresco models accord with the results of inter-specific co-occurrences. Moreover, the latter method revealed a link between H. vernicosus and the occurrence of disjunctly occurring boreal sedges, suggesting the relic nature of H. vernicosus habitats at these locations.