In the cuc2 cuc3 double mutant of Arabidopsis thaliana the regular spiral Fibonacci phyllotaxis is disrupted and flower pedicels are fused to the inflorescence stem in the mature shoot regions. Burian et al. investigate phyllotaxis and geometry of shoot apices, and growth of the young stem surface, and show that CUC2 and CUC3 genes are crucial for the regulation of growth and cell divisions during post-meristematic shoot development, but not for regular flower primordia positioning at the apex. The main mutation effect is the formation of pedicel–stem fusions, most likely related to slightly delayed appearance of the primordium boundary. Fusions and increased density of flower primordia at the mutant shoot apex are involved in alteration of the axial positioning of flowers.