The genesis of phyllotaxis, which often is associated with the Fibonacci series of numbers, is an old unsolved puzzle in plant morphogenesis. Here, we show that disruption of an Arabidopsis topoisomerase (topo) I gene named TOP1 affects phyllotaxis and plant architecture. The divergence angles and internode lengths between two successive flowers were more random in the top1 mutant than in the wild type. The top1 plants sporadically produced multiple flowers from one node, and the number of floral organ primordia often was different. The mutation also caused the twisting of inflorescences and individual flowers and the serration of leaf margins. These morphological abnormalities indicate that TOP1 may play a critical role in the maintenance of a regular pattern of organ initiation. The top1 mutant transformed with the RNA interference construct for TOP1ß, another topo I gene arrayed tandemly with TOP1, was found to be lethal at young seedling stages, suggesting that topo I activity is essential in plants.