The shoot apical meristem (SAM) generates all above-ground organs throughout the life of plants. The development and maintenance of the SAM are crucial for building the plant architecture. The spatiotemporal patterning of lateral organs (leaves and flowers), called phyllotaxis, is one of the best-characterized self-organizing systems and has long been proposed to be driven by inhibitory fields generated by the existing organs and blocking new initiations in their vicinity. Recent years have seen impressive progress in our understanding of the molecular mechanisms controlling SAM function, and on how these mechanisms act in phyllotactic patterning. In this chapter, we first review the regulation of SAM stem cell activity and discuss how feedback signals coming from the differentiated organs affect stem cell homeostasis. Then we highlight experimental and theoretical works that have revealed the chemical and biophysical factors acting in the regulation of phyllotaxis. Finally, we summarize the important roles of SAM geometry in phyllotaxis.