Sequences of the chloroplast genes matK and rbcL and nuclear ribosomal ITS2 were used for phylogenetic analyses of Berberidaceae. Three major clades were recognized, corresponding to the chromosome base numbers x = 6, 7, and 8/10. Bongardia was sister to the clade containing Achlys and the Podophyllum group, which consists of Diphylleia, Sinopodophyllum, Podophyllum, and Dysosma. The estimated times of divergence of six disjunct genera between Eurasia and North America ranged from 7.5 ± 2.3 Ma to 1.0 ± 0.7 Ma. The intercontinental disjunct lineages of Berberidaceae may have originated in eastern Asia and then migrated to Europe and North America. However, long-distance dispersal may explain the distribution pattern of Achlys. Desert xerophytes of Berberidaceae in southwestern Asia originated in response to the advent of dry climate at different times; Bongardia diverged from its closest relatives at 46.5 ± 3.6 Ma, whereas Leontice differentiated from Gymnospermium at 10.3 ± 3.2 Ma.