Individuals of Pediomelum tenuiflorum, “wild alfalfa”, from disjunct populations in Nebraska vary extensively in their overall gestalt. Those in the western and central part of the state have a very slender growth habit, with thin stems and few, small flowers; whereas, those in the southeast have a very robust growth habit with heavy-looking stems and many tightly clustered flowers. For nearly 200 years, taxonomists have alternated between splitting P. tenuiflorum into two species, with the many-flowered morphotype named P. floribundum, and lumping all the morphological variants into one species as they are now. In this study, we investigated morphological and molecular characters that could be used to clarify taxonomic classifications of these morphotypes. We measured 10 morphological characters on 51 specimens and sequenced nearly 300,000 nucleotide characters on the Illumina platform from three cellular genomes in seven samples of Pediomelum plus an outgroup taxon. Results revealed six significantly different morphological characters but ambiguous evolutionary histories of the plastid and mitochondrial genomes in P. tenuiflorum. Our complete plastid genomes and genes and noncoding regions of the mitochondrial genome may be used as a foundation for studying the evolutionary histories of these genomes. Additionally, we identified seven highly variable genomic regions in the chloroplast genome upon which a molecular phylogenetic investigation on an expanded set of samples from across the species’ geographic distribution can be conducted to further define the taxonomic placements of P. tenuiflorum and P. floribundum.