Species delimitation is problematic in many plant groups and among the mosses, Sphagnum is one of the more contentious genera because of high levels of morphological variation. The allopolyploid species, Sphagnum majus, comprises one such problematic complex. Two morphologically differentiated but overlapping subspecies have been described. We conducted morphometric and molecular analyses with samples from around the Northern Hemisphere to test for phenotypic and phylogenetic differentiation between the subspecies. Although field collections of the two species can be statistically differentiated morphologically, there is substantial overlap. Genome-scale molecular data do not suggest any differentiation between S. majus ssp. majus and ssp. norvegicum, including samples assigned to the two taxa from sympatric sites. Sequence data from the plastid genome were employed to infer parentage of allopolyploid S. majus. Our results support the hypothesis that S. annulatum is the paternal parent and S. cuspidatum is the maternal parent. We conclude that the morphological differences between them are either plastic responses to habitat heterogeneity or segregating genetic variation within a single taxon. Formal taxonomic recognition of two taxa is not supported by our molecular data.