Bryophytes have sometimes ambiguous morphological diagnostic features, so molecular markers can prove a useful tool in systematics, even more in a well known morphologically variable moss such as Hypnum cupressiforme. This paper focuses on genetic diversity in the H. cupressiforme complex inferred by ISSR markers and ITS and trnL sequences. Shoots from nine Italian populations of H. cupressiforme and from five other species included in the complex were analysed. Sequence divergence among the analysed species is very low, with the exception of Hypnum jutlandicum. The neighbour joining tree based on ISSR data shows that all the H. cupressiforme samples do not merge into a distinct cluster, but spread on the whole dendrogram. Molecular variance is partitioned more within-than between-species. Therefore, the genetic variation detected by ISSR at intra-and inter-specific level appears to be, to a large extent, the result of the individual variation, suggesting that the polymorphism detected appears poorly informative at a taxonomic level. Our results suggest that morphological variation of the H. cupressiforme complex does not always correspond to genetic diversity, and highlight a major molecular divergence of H. jutlandicum within the complex.