The harvestmen Caddo agilis Banks 1892 and C. pepperella Shear 1975 (Caddidae, Caddinae) share a disjunct distribution in eastern Asia and eastern North America that has been attributed to either recent (Pleistocene) evolution of a C. pepperella morph from C. agilis in each region or to a pre-glacial separation within each of two established species. The present study used 2,130-base sequences from two nuclear protein-coding genes (EF1α, Pol II) to test the phylogenetic predictions of both hypotheses using representatives from the two Caddo species from both regions and two acropsopilionine outgroup species. The results supported the hypothesis that the two Caddo species were distinct prior to their respective biogeographic disjunctions; C. agilis and C. pepperella were each recovered as monophyletic and each appears to have undergone separation into Asian and North American groups.