Identifying discrete taxa within species complexes is an important issue in systematic and evolutionary biology. An understanding of the genetics of closely related species can highlight complex evolutionary processes, but a scarcity of morphological characters that separate the species fuels discussions about the usefulness of formally recognizing them. One controversial recent issue has been the division of the “globally distributed” Sphagnum magellanicum into multiple morphologically cryptic taxa. With the latest description of two new species, this makes a total of four species in North America: S. diabolicum, S. divinum, S. magniae and S. medium. Sphagnum in general, and the S. magellanicum complex in particular, has been developing as a model group for ecological genomics, so it is important to learn if and how frequently these morphologically cryptic species occur sympatrically, and about possible differences between them in microhabitat and climate niches. For this reason, we developed and tested barcode markers using a set of primers that accurately classify specimens to the segregate species. Identifications involve DNA extractions, barcode amplification, and running the amplified DNA out on an agarose gel, but no sequencing. 884 individuals from 819 collections were studied from 120 different sites, with samples spanning North America from Florida to Quebec and west to Michigan, Wisconsin, Minnesota, British Columbia, Alberta, and Washington. From 41 sites with more than five samples, we identified nine sites with three sympatric species and another 16 sites with two species. We found that these species have somewhat different though overlapping niches. Although they can be very difficult to consistently distinguish morphologically, the species maintain their genetic distinctiveness and appear to represent “good” biological species.