To clarify long-standing disagreements about the taxonomic and phylogenetic status of Sphagnum macrophyllum and S. cribrosum, twenty-five samples of S. macrophyllum and twenty-four of S. cribrosum, including the rare wave-form morphotype, were sampled from ten states of the eastern United States. The data set included intensive sampling from three populations in North Carolina. Three anonymous genomic regions (rapdA, rapdB and rapdF) were sequenced for all the samples; two (nuclear) LEAFY introns (LEAFY1 and LEAFY2) and one chloroplast locus (trnG) were sequenced for all the samples excluding the twenty-two within-population North Carolina samples. The results showed that S. macrophyllum and S. cribrosum are reciprocally monophyletic with maximum parsimony bootstrap support and significant Bayesian posterior probabilities. Genetic analyses based on neutral coalescence models suggest that the simplest allopatric speciation model—the isolation model with no subsequent gene flow and constant population sizes—cannot be rejected. Nevertheless, some topological conflicts among loci suggest the possibility of limited interspecific hybridization. This study also showed that the morphologically distinctive wave-form is nested within S. cribrosum and wave-form samples from Singletary Lake make up a clade of nearly identical plants. Interestingly, S. macrophyllum and S. cribrosum are morphologically highly similar but are reciprocally monophyletic and highly differentiated, whereas the unique and morphologically divergent wave-form is genealogically derived from within normal S. cribrosum.