Speciation processes in vascular plants are frequently not well resolved or agreed upon. They are however essential to our general understanding of the evolutionary processes that lead to diversification. Determining the juncture at which a genetically and/or morphologically divergent population becomes a unique species can be challenging, especially with respect to recent divergences and closely related taxa where issues such as incomplete lineage sorting may bring about confounding results. To complicate our theoretical disagreements on species definitions, different models inferring species boundaries may accordingly lump or split species. Using multiple lines of evidence to define species boundaries can greatly improve species inference and preclude erroneous taxonomic groupings. Taxa in the Cymopterus terebinthinus (Apiaceae) species complex have long puzzled botanists owing to their similar yet diverse, consistently recognizable morphotypes. These morphotypes are often found in generally well-defined geographical subregions of varying habitat types. To further complicate taxonomic groupings in this species complex, previous phylogenetic studies are interpreted to show that varieties in Cymopterus terebinthinus are not monophyletic. We aim to clarify species boundaries and infer evolutionary relationships in the Cymopterus terebinthinus species complex using phylogenetic inference paired with ecological parameters, morphology, and biogeography. We apply the genealogical species concept to guide our interpretations of species boundaries in this group. To test this, we used target capture with the angiosperms353 bait kit and next generation sequencing. We performed phylogenetic analysis with maximum likelihood and coalescent based species delimitation models. We also used corroborating evidence based on analysis of ecological variables to better understand factors related to phylogenetic groupings. We find that Cymopterus terebinthinus and its varietal infrataxa comprise a monophyletic clade that includes Cymopterus petraeus. We also find that geographical location is typically the best predictor of phylogenetic placement, meaning that in the large majority of samples analyzed, defined clades largely correspond to previous varietal assignments. Our findings argue that gene flow is likely actively occurring amongst populations in peripatric and sympatric proximity. Additionally, species differentiation processes are likely actively producing divergence within biogeographical regions.