Brassica oleracea L. vars, italica (broccoli) and botrytis (cauliflower) both undergo developmental arrests which result in heading phenotypes. We characterized these arrested tissues at the morphological and molecular levels, and defined the developmental changes that ensure after arrest has been broken. We found that the order of floral organ initiation and the positions of resulting floral organ primordia in this species in some respects from that of Arabidopsis, which is a member of the same family, Brassicaceae. We also cloned homologs of the Arabidopsis floral homeotic genes APETALA1 (AP1) and APETALA3 (AP3) from B. oleracea and characterized their expression patterns. We found that the AP1 homolog was expressed in some of the meristems of arrest-stage cauliflower, providing evidence that this tissue is florally determined. In broccoli, both the AP1 and AP3 homologs were expressed. However, the spatial pattern of expression of the broccoli AP1 homolog differed from that of Arabidopsis. In addition we identified a homolog of the CAULIFLOWER (CAL) gene, BoiCAL, from broccoli. The predicted amino acid sequence indicated that the BoiCAL gene product does not contain the mutation thought to be responsible for the early arrest exhibited in cauliflower (Kempin et al. 1995), but contains other changes that might play a role in the broccoli heading phenotype.