Background: Differentiating plant species is complex, complicated by morphological similarities that confound species’ delineation. For hundreds of years, researchers have used herbarium specimens to study plant morphology, and over the last forty years, these samples have also served as material for molecular phylogenetic research. Taxonomists have alternately split and combined morphotypes of Pediomelum tenuiflorum for two centuries. With samples of P. tenuiflorum from across its distribution, this research aimed to: 1) infer a robust phylogeny using molecular data, i.e., gene sequences from chloroplast and nuclear genomes, 2) assess genetic diversity using molecular markers, specifically Inter Simple Sequence Repeats (ISSRs), 3) provide evidence to support the taxonomic placement and possible splitting of P. tenuiflorum, and 4) identify consistent morphological characteristics using a correlation matrix to distinguish among the morphotypes.

Results: Striking morphological differences among the individuals of P. tenuiflorum from across the species’ distribution resulted in more than two morphotypes. Both phylogenetic data and ISSR results suggest hybridization is occurring among genetically and morphologically distinct members of P. tenuiflorum and with other species in the genus Pediomelum. This study reports the first ISSR markers used to assess genetic diversity in Pediomelum species.

Conclusions: Morphological and genetic variation exists across individuals of Pediomelum tenuiflorum but not in monophyletic groups that support splitting the morphotypes into multiple species. Future investigations into chromosome numbers might reveal polyploidization in the lineage, and phylogenies estimated from low-copy nuclear genes could elucidate hybridization pathways.