Plant architecture includes patterns of arrangement of vegetative organs and flowers that may be difficult to describe because of the modular nature of plant growth. We disentangle the terminological issues and provide a case study of a clade of Polygonaceae family. The study focuses on the characteristics of thyrses, reproductive shoots, and shoot systems in 37 species of Atraphaxis, 5 species of Persepolium, and Bactria ovczinnikovii from arid regions of Eurasia using a phylogenetic approach. Based on the plastid phylogeny, parsimonious reconstructions of the evolution of 16 traits were obtained. Three types of perennial shoot systems were identified: perennial systems formed by reproductive (Type I) or vegetative (Type II) shoots, or by both (Type III). Type I was found in Persepolium, Bactria, and a basal subclade of the clade Atraphaxis, and was considered the plesiomorphic state. Type II was found in several distal subclades of the Atraphaxis clade, and was derived from Type I, while Type III was found in a distal subclade, corresponding to the section Atraphaxis. The characteristics of inflorescences and shoots differentiate Persepolium from Bactria and Atraphaxis and provide new data for the classification of the latter genus. Our findings confirm the heterogeneity of the section Tragopyrum, which includes species with Types I and II shoot systems, as well as the isolation of sections Atraphaxis and Physopyrum, which differ in the structure of their thyrses.