All plant shoots can be described as a series of developmental modules termed phytomers, which are produced from shoot apical meristems. A phytomer generally consists of a leaf, a stem segment, and a secondary shoot meristem. The fate and activity adopted by these secondary, axillary shoot meristems is the major source of evolutionary and environmental diversity in shoot system architecture. Axillary meristem fate and activity are regulated by the interplay of genetic programs with the environment. Recent results show that these inputs are channeled through interacting hormonal and transcription factor regulatory networks. Comparison of the factors involved in regulating the function of diverse axillary meristem types both within and between species is gradually revealing a pattern in which a common basic program has been modified to produce a range of axillary meristem types.