In 2013, a new species of clover endemic to Kentucky was described. This species, Trifolium kentuckiense (Fabaceae), has yet to be placed in a phylogeny but is hypothesized to be most closely related to T. reflexum based on morphology. We present phylogenetic evidence from the nuclear (ITS) and plastid genomes (trnL and ndhA introns) that T. kentuckiense is a member of a clade of seven Trifolium species native to eastern North America. Within this clade, T. kentuckiense is strongly placed in a clade with three other annual/biennial Trifolium species (T. bejariense, T. carolinianum, and T. reflexum); it is sister to T. reflexum, although support for this relationship is weak. Our results support previous findings that suggest the ndhA intron is much more variable than the trnL intron in the Eurosid I clade. The ndhA intron contained over twice the number of parsimony informative characters when compared to the trnL intron, though ITS was more variable than either region. We also provide a dichotomous key to native and nonnative members of Trifolium for Kentucky and its surrounding states. We suggest determinations of historic specimens of Trifolium, particularly those identified as T. reflexum, be reassessed to obtain localities that may still support populations of this recently described species. We also provide guidance on when and in what habitats to search for new populations of this extremely rare taxon.