Structural features of the shoot system and inflorescence are the most important morphological features, on which plant systematics are based. The present review provides information on the genetic control of shoot morphogenesis in the model plant Arabidopsis thaliana. The results obtained made it possible to reveal a small group of genes responsible for the main taxonomic features of the shoot structure in this species. Cloning of these genes opened new avenues for directed search of homologous genes in other plants. Comparative analysis of the shoot structure and studies of the function and expression of these genes in various plants suggest that morphological evolution may be based on changes in the pattern of expression of single regulatory genes.