The Capparaceae have long been considered closely related to and have often been included in the Brassicaceae, the mustard family (APG, 1998), in part because both groups produce glucosinolate (mustard oil) compounds.

Subsequent molecular studies[3] support Capparaceae sensu stricto as paraphyletic with respect to the Brassicaceae.

Several more genera of the traditional Capparaceae are more closely related to other members of the Brassicales, and the relationships of several more remain unresolved.

[4] Based on morphological grounds and supported by molecular studies, the American species traditionally identified as Capparis have been transferred to resurrected generic names.

[5] Based on recent DNA-analysis, the Capparaceae are part of the core Brassicales, and based on limited testing, the following tree represent current insights in its relationship.