A major problem in taxonomy is to determine if morphological variation in field-collected specimens is caused by genetic differentiation, and therefore corresponds to evolutionary distinct units, or is caused by environmental variation acting on a single interbreeding population. To evaluate the effect of environmental variation on the taxonomy of the moss genus Ceratodon, we compared biometric analyses based on 22 morphological characters on both field-collected plants and cultivated plants to a clustering based on DNA sequence and genome size data published previously. We sampled Ceratodon species from mountainous areas of the Mediterranean region, and other mountain regions and lowlands, mostly from southern Europe. We found that the expression of several gametophytic traits changed between field and laboratory conditions, confirming that environmental variability complicates taxonomic inferences, and suggesting that some characters should be used with caution in distinguishing among species. However, consistent with the genetic and flow cytometry data, we found a clear biometric discontinuity between some plants collected from southern Spain, and those from other parts of the world. Samples considered of hybrid origin, based on genetic data, were morphologically indistinguishable from plants from the southern Spanish mountains. Integrative taxonomy based on genetic, genome size and morphological data unambiguously support the recognition of a new species, Ceratodon amazonum. These data also suggest that the previously recognized C. conicus is a recombinant between C. amazonum and C. purpureus and is considered here to be a nothospecies, for which an epitype is designated because the lectotype is demonstrably ambiguous.