Morphology and ITS relationships are compared for 111 Sciuro-hypnum specimens, 95 of which belong to S. curtum, S. hylotapetum, or the S. reflexum complex. In the latter, S. reflexum is probably ancestral. Within the S. reflexum complex ITS haplotype relationships are congruent with morphology for S. brotheri, S. dovrense, S. glaciale, and S. ornellanum, and support the recognition of the two new species S. sinolatifolium and S. sichuanicum, whereas incongruence occurs for several species. In an ITS haplotype context, S. tromsoeense and S. latifolium are resolved as polyphyletic, and S. altaicum, some specimens of S. oedipodium, and S. curtum–S. starkei intermediates cannot be distinguished from S. reflexum. Sciuro-hypnum fuegianum is molecularly identical and morphologically similar to S. glaciale, and is considered conspecific with the latter. There is no evidence to suggest that ITS a priori is more reliable than morphology, and we therefore suggest that the abundant incongruent patterns reflect either 1) a young age in terms of number of generations in relation to the rate of ITS differentiation and associated incomplete lineage sorting and occasional hybridization events, 2) a faster rate of morphological than ITS evolution, 3) the existence of many lineages that are propagated by selfing, or 4) regional differences in extinction rates during the Pleistocene glaciations. However, additional information is required to decide which of these is/are most important. Finally, S. squarrosum, a morphologically distinct species that molecularly belongs outside the S. reflexum complex, is described as new.