Documenting biodiversity, at and below the species level, is a persistently challenging task for biologists. Poor understanding of biodiversity may lead to incorrect interpretations of observed variation. The underlying basis of variation can be understood by quantifying multiple sources of information. Nine morphometric characters and plastid DNA sequences (2511 bps) were quantified in a highly variable orchid species, Platanthera dilatata, to evaluate taxonomy of the three named varieties and to understand patterns of evolution. Three morphological groups, identified in a cluster analysis, were distinct in multiple floral traits. Additionally, the three clusters were consistently genetically divergent as indicated by infrequent haplotype sharing, significantly different haplotype frequencies, and significant values of the genealogical sorting index. This level of genetic divergence suggests three species rather than varieties in this complex. The divergent floral morphologies suggest that pollinator-mediated selection may be a driving factor for speciation in this complex.