Accurate species delimitation is paramount to studies of biodiversity and ecology. Lineage concepts applying coalescent approaches to species delimitation have become increasingly popular, yet have been questioned recently in their ultimate value, and for conflating species boundaries with population structure. The ‘Phenophyletic Species Concept’ explicitly considers both lineages and ecological ‘role’ shifts and provides an opportunity to incorporate ecologically meaningful data from multiple sources in studies of species boundaries. Here, the Phenophyletic Concept was applied to a problematic group of mycoheterotrophic orchids, the Corallorhiza striata complex, by analyzing genomic, morphological, phenological, reproductive-mode, niche, and fungal host data. Our recently developed method for generating genomic polymorphism data–ISSRseq–demonstrates strong evidence for four distinct lineages. There is evident divergence in morphology, phenology, reproductive mode, and fungal associates among the lineages; however, none of the datasets aside from genomic data fully satisfy the condition of a significant ‘role’ shift, which requires evidence of fixed differences in the ‘extended phenotype.’ The four principal lineages identified in the current study are thus recognized at the level of variety, short of comprising different species. This study represents the most comprehensive application of the Phenophyletic Species Concept to date, and illustrates the advantages of such an approach.