We tested the hypothesis that Uniola paniculata populations are divided into eastern and western lineages, with the primary geographic break at the southern tip of Florida, as observed in codistributed animal taxa. We asked whether the geographic distribution of chloroplast DNA (cpDNA) variation in U. paniculata corresponds to 1) genetic structure in nuclear variation reported in previous studies, and 2) the geographic distribution of morphological adaptive traits reported in previous studies. We sampled 66 populations and performed phylogeographic analyses using sequence variations in maternally inherited cpDNA. We reconstructed the intraspecific phylogenetic network with TCS software and identified phylogeographic breaks in the species using Monmonier’s algorithm. Analyses identified 6 cpDNA haplotypes and 2 major lineages: eastern (Atlantic) and western (Gulf), with a phylogeographic break at the southern tip of Florida. The data suggest U. paniculata survived the last glacial maximum (LGM) in southern refugia. Following the LGM, differential leading-edge recolonization explains the current distribution of haplotypes into 2 lineages. Populations containing a haplotype from outside its native range are likely due to human-mediated transplantation. The genetic structure of cpDNA variation has weak correlation with nuclear DNA variation, and there is partial concordance between the geographic distribution of cpDNA and morphological variation.