Locus-specific primers were designed to amplify the homologues LEGCYC1A and LEGCYC1B of the snapdragon (Antirrhinum majus) floral symmetry gene CYCLOIDEA in the genistoid legumes Lupinus nanus and Cadia purpurea. These primers were tested successfully in a range of genistoid taxa. Sequence comparison between L. nanus and L. angustifolius revealed that these CYCLOIDEA-like genes provide up to four times as many variable characters as the ribosomal internal transcribed spacers (ITS) at this taxonomic level. These genes are therefore potentially useful for studying evolutionary relationships between closely related species within the genistoid clade of legumes, which contains many large and diverse genera. Comparisons between L. nanus, Cadia purpurea and Calpurnia aurea LEGCYC sequences show that these genes may also be useful for phylogenetic studies between genera in this large clade of 1800 species.