The present study aimed to develop a robust, extensively sampled phylogenetic hypothesis across all species in Leavenworthia and Selenia using chloroplast (psbJ—petA) and nuclear encoded (nrDNA ITS and LUMINIDEPENDENS) DNA sequence data. Parsimony and maximum likelihood methodologies were employed. Strong maximum likelihood bootstrap and parsimony jackknife support were recovered for the monophyly of the sister pair Leavenworthia plus Selenia and for the respective monophyly of each genus. Leavenworthia and Selenia are hypothesized to have diverged in the Ozark Mountains and results from an analysis of branch lengths leading to Leavenworthia and Selenia clades are consistent with Leavenworthia having diversified more recently than Selenia. Polyploidy and extensive aneuploidy complicate the interpretation of chromosomal evolution within and between these genera. Comparative results from phylogenetic analyses indicate that L. aurea and L. texana are hybrids with a shared set of putative parents. Lastly, patterns of diversification within Leavenworthia appear to have included a minimum of three transformations from self-incompatible to self-compatible systems.