The geographical distributions of the two cryptic species of the wetland moss Hamatocaulis vernicosus were mapped for western, central and northern Europe, based on identifications of the two by the nuclear ITS1 + 2 and the plastid rpl16 and trnL–trnF. The distributions of the two cryptic species overlap to a large extent. However, in the west and south-west only cryptic species 1 is present, whereas in the boreal north only cryptic species 2 occurs, which agrees with its distribution in Scandinavia. Despite these differences in distribution, no differences between the two cryptic species were revealed in habitat water chemistry, elevation distribution or climatic niches. The difference in distribution therefore suggests that cryptic species 1 could have survived the glacial period in southern Europe and cryptic species 2 in northern or eastern Europe. However, the studied molecular markers did not reveal geographical patterns suggesting origins in different glacial refugia. Although populations of both cryptic species have decreased in large portions of western Europe, a significantly negative Tajima’s D may reflect the long-term expansion south of Scandinavia since the glacial bottleneck, potentially correlated with the expansion of earlier extensive agricultural management of wetlands.