This study provides the first report that Sphagnum centrale and S. henryense are allopolyploids. Microsatellites show S. henryense and S. palustre to be conspecific. In contrast, they show S. centrale to be genetically distinct from S. palustre s.l. In addition to differences in alleles and allele frequencies, the patterns of observed heterozygosity across 17 microsatellite markers also differed between S. centrale and S. palustre s.l. This represents a dimension of genetic differentiation that is not detected or addressed by statistical approaches such as AMOVA or Principal Coordinates Analysis. The patterns of microsatellites further provide preliminary evidence suggesting that S. centrale and S. palustre have one parental taxon in common and differ in the second.