Sequences of cpDNA (rbcL) were determined for 94 species and of ncDNA [ITS 1 + 2 regions (internal transcribed spacer) of rDNA] for 75 species representing mainly the papilionoid tribes Sophoreae, Thermopsideae Podalyrieae, Liparieae, Crotalarieae, and Genisteae. Sequence data were used to reconstruct the underlying molecular phylogeny. Several clusters and furcations were identical in the rbcL and ITS trees of the Papilionoideae, indicating that a reticulate evolution due to past hybridization of members from different tribes and genera is unlikely: The Sophoreae (especially Styphnolobium japonicum (syn. Sophora japonica) and Sophora secundiflora) are positioned at the base of the papilionoid tree, whereas some other Sophora species (Sophora davidii, flavescens, jaubertii, microphylla) are closely related to Thermopsideae/Podalyrieae. The Thermopsideae/Podylyrieae cluster (including Liparieae) shares ancestry with the Crotalarieae and Genisteae. Argyrolobium (African taxa) and Melolobium cluster between Crotalarieae and Genisteae. In the Genisteae three clusters are apparent: the monophyletic genus Lupinus, the Cytisus-, and the Genista-group. According to this analysis, the Cytisus-complex includes Cytisus, Lembotropis, Chamaecytisus, Spartocytisus, and Calicotome. The Genista-group consists of Genista, Teline, and Chamaespartium sagittale. Other genera (e.g., Adenocarpus, Argyrocytisus, Cytisophyllum, Erinacea, Laburnum, Petteria, Retama, Spartium, and Ulex) could not be attributed unequivocally to the Cytisus or Genista complex.