The APG IV system of 2016 recognises the family and places it in the order Ranunculales in the clade eudicots.

[2] In some older treatments of the family, Berberidaceae only included four genera (Berberis, Epimedium, Mahonia, Vancouveria), with the other genera treated in separate families, Leonticaceae (Bongardia, Caulophyllum, Gymnospermium, Leontice), Nandinaceae (Nandina), and Podophyllaceae (Achlys, Diphylleia, Dysosma, Jeffersonia, Podophyllum, Ranzania, Sinopodophyllum).

Genera are displayed in the following cladogram Alloberberis C. C. Yu & K. F. Chung Berberis L. including Mahonia Nutt.

— heavenly bamboo (eastern Asia from the Himalaya to Japan) Caulophyllum Michx.

— inside-out flower (western U.S.) Jeffersonia W. Bartram — twinleaf Plagiorhegma Maxim.