The genus Ponera is a lineage of leaf litter ants, with a center of diversity in the Indo-Australian region. Two species occur in the New World; however, uncertainty exists with regard to their biogeographic origins and species limits, especially for isolated cloud forest populations in Middle America. We investigate the geographic distribution, phylogeny, and phylogeography of these two species to better characterize the American ant fauna and to gain insight into the biogeography of taxa that span hemispheres. Sequencing of Ultra-Conserved Element (UCE) loci was used to infer phylogenetic relationships, estimate divergence dates, and test species boundaries. The widespread native species P. exotica and P. pennsylvanica are each more closely related to Old World relatives than they are to each other, implying two independent colonizations of the New World. Ponera pennsylvanica is most closely related to the European species P. coarctata, while P. exotica is related to a clade of Indo-Australian species. Ponera pennsylvanica is abundant throughout the eastern USA, with scattered occurrences further west. Ponera exotica occurs from the southern USA to Nicaragua. Both species have alate and ergatoid queens. Sequenced specimens from multiple populations of P. exotica reveal a pectinate phylogeographic structure, from north to south, with the potential for multiple cryptic species. The southern USA to Middle America distribution pattern of P. exotica mirrors that of many plant and animal species and may be the result of climatic cooling in the Pliocene followed by repeated glacial cycles in the Pleistocene, which condensed and fragmented mesic forest habitat.