Within Sphagnum cribrosum, a dioicous aquatic peatmoss, a unique morphological variant (the ‘waveform’), found at only two lakes in North Carolina, has a branching architecture that is extremely differentiated from anything otherwise known in Sphagnum, although the plants are microscopically indistinguishable from S. cribrosum. At one site where the two morphologies co-occur, 60 years of field observations demonstrate the persistence of each morphology, even where the two forms grow intermixed. We conducted a reciprocal transplant experiment in which waveform and normal plants maintained their divergent morphologies for 8 months. We sampled populations throughout the range and conducted genetic and phylogenetic analyses with microsatellite markers and DNA sequences to investigate the genetic context of the waveform morphology within S. cribrosum. Haplotype networks from DNA sequences showed the two waveform populations are separated by 11 substitutions across three loci. Microsatellite analyses using nonparametric clustering and admixture models also indicated genetic dissimilarity between genotypes with waveform morphology at the two lakes. Both molecular datasets suggest that the waveform morphology had at least two independent origins, despite the proximity of the two lakes where it occurs uniquely. Given the clonal nature of the waveform, it is unlikely to form a cohesive evolutionary lineage deserving of taxonomic status. The analysis also revealed a genetically diverse population in Georgia as the potential source of variation found in all other populations of S. cribrosum. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106, 137–153.