The RABBIT EARS (RBE) gene has been identified as a regulator of petal development in Arabidopsis thaliana. We find that second-whorl petals in rbe mutants can be replaced with staminoid organs, stamens or filaments and that some rbe flowers have increased numbers of sepals and exhibit fusion of sepals. We show that these rbe defects are due to AGAMOUS (AG) misexpression in the second whorl. Consistent with its role in maintaining the spatial boundary of AG expression, rbe enhanced the second-whorl defects present in ap2-1, lug-1 and clf-2 mutants. In the development of second-whorl organs, RBE acts in the same pathway and downstream of UNUSUAL FLORAL ORGANS (UFO). Enhanced first-whorl organ fusion in ap2-2 rbe-3, ant-4 rbe-3 and cuc2-1 rbe-3 double mutants supports an additional role for RBE in organ separation. RBE thus acts to maintain two different types of spatial boundaries in young flowers: boundaries between organ primordia within a whorl and boundaries of homeotic gene expression between whorls.