The taxonomically problematic Drepanocladus aduncus (Hedw.) Warnst. s.l. has either been treated as a single phenotypically variable species or as including a variable number of taxa at different levels. In this investigation, the molecular variation within the D. aduncus complex is studied based on the internal transcribed spacer (ITS), the trnL (UAA) 5' exon-trnF (GAA) region, and tRNA-Gly. Relationships among more than 100 specimens are studied by means of neighbor joining (ITS; while potential hybridization was revealed), maximum parsimony (chloroplast markers), and haplotype network reconstruction (all markers). The complex exhibits considerable haplotype variation, but the variation is uncorrelated with recognized taxa. On the other hand, the studied material suggests that a geographic component is present in the variation, especially in Europe. The geographical distributions of some haplotypes suggest a possible relationship with the glacial history of Europe, although this needs to be further investigated based on a larger sample before any firm conclusions can be drawn. Two molecularly strongly deviating plants were revealed; these were collected in salt water streams at high elevations in South America.