Despite the widespread usage of the term ‘species,’ considerable debate exists surrounding what criteria should be applied to recognize distinct evolutionary units. Most species have historically been recognized based on morphology, with modern species concepts recognizing that isolation among diverging taxa, whether it is reproductive, ecological, morphological, or genetic isolation, is a major driver of speciation. However, which specific criteria should be applied to justify the recognition of any species, and whether different criteria lead to the homologous recognition of taxa is not well addressed in the literature. In the present work, genetic data was collected from two Acmispon species (A. argophyllus and A. dendroideus; Fabaceae), representing a total of 6 varieties, endemic to the California Channel Island. The California Channel Islands represent a unique system to study the role of isolation in divergence due to variability in island age, size, and separation, and the proximity of the entire island chain to the continental mainland. Data was collected from nuclear microsatellites, a low copy nuclear gene, and the chloroplast genome, to investigate evolutionary relationships at multiple evolutionary time depths. Despite clear morphological differences, both nuclear and chloroplast DNA sequence datasets failed to resolve the two Acmispon species as distinct entities, implying multiple independent mainland to island colonization events and significant amounts of incomplete lineage sorting. However, the nuclear microsatellite data clearly resolves A. dendroideus as two distinct genetic units, and A. argophyllus as four genetic units, each with an affinity to different mainland locations and taxa. This research demonstrates that the morphological characteristics of an organism can be misleading with regards to its’ evolutionary history, and that the characteristics of a genetic dataset (i.e. mutation rate) impacts the evolutionary groups resolved by summarizing relationships at different evolutionary time depths.