Celtis tenuifolia is a threatened tree in southern Ontario. Although it is common further south, only six disjunct sites in Ontario exist, and these populations are susceptible to extinction due to habitat loss. It is difficult for conservation managers to distinguish C. tenuifolia from related Celtis species morphologically, and taxonomists have questioned species limits in this group. Using microsatellite markers and flow cytometry, we assessed the relationship between genetic diversity, ploidy, and morphology in this genus. We have determined that C. tenuifolia is an apomictic allotriploid, and flow cytometry provides a reliable tool for distinguishing it from the sexual diploids C. occidentalis and C. laevigata. Furthermore, the same C. tenuifolia genotypes occur in a variety of habitats, demonstrating remarkable phenotypic plasticity. The results of this assessment will direct management of C. tenuifolia, providing reliable identification tools, and resolving concerns around hybridization and the risks of inbreeding depression.