Following on emerging understanding of the diversification process, many recent workers have considered infraspecific taxa as valuable for formally recognizing incompletely speciated entities. The distinction between a species and an infraspecific taxon represents a fundamentally subjective weighting of evidence, yet this points further to the need for an evidential basis for these decisions. We explore these concepts in Heuchera longiflora (Saxifragaceae), which is morphologically variable and has a disjunct range across several physiographic provinces in the eastern U.S. using a tiered sampling approach and a combination of Sanger and next generation sequencing (NGS) techniques. We investigated 56 populations with seven markers to investigate population structure, and for a subset of 12 representative populations we sequenced 277 nuclear markers to characterize gene tree discord. Using a variety of methods to overcome high levels of gene conflict, we find evidence for the traditionally recognized taxa H. longiflora var. longiflora and H. longiflora var. aceroides in molecular and morphological data partitions. Our results comprise a case study on the use of multiple sources of data and analytical methods to delimit infraspecific taxa.