The genus Cryptopone Emery contains 25 species of litter and soil ants, 5 of which occur in the Americas. Cryptoponegilva occurs in the southeastern U.S.A. and cloud forests of Mesoamerica, exhibiting an uncommon biogeographic disjunction observed most often in plants. We used phylogenomic data from ultraconserved elements (UCEs), as well as mitogenomes and legacy markers, to investigate phylogenetic relationships, species boundaries, and divergence dates among New World Cryptopone. Species delimitation was conducted using a standard approach and then tested using model-based molecular methods (SNAPP,  BPP, SODA, and bPTP). We found that Cryptopone as currently constituted is polyphyletic, and that all the South American species belong to Wadeura Weber, a separate genus unrelated to Cryptopone. A single clade of true Cryptopone occurs in the Americas, restricted to North and Central America. This clade is composed of four species that originated ~4.2 million years ago. One species from the mountains of Guatemala is sister to the other three, favoring a vicariance hypothesis of diversification. The taxonomy of the New World Cryptoponeand Wadeura are revised. Taxonomic changes are: Wadeura Weber is resurrected, with new combinations W. guianensisWeber, W. holmgreni (Wheeler), and W. pauli (Fernandes & Delabie); C. guatemalensis (Forel) (rev. stat.) is raised to species, and includes C. obsoleta (Menozzi) (syn. nov.). The following new species are described: Cryptopone gilvagrande, C. gilvatumida, and Wadeura holmgrenita. Cryptopone hartwigi is transferred to Fisheropone (n. comb.). Cryptopone mirabilis (Mackay & Mackay 2010) is a junior synonym of Centromyrmex brachycola (Roger) (syn. nov.).