The long-held notion that the sporophyte shoot is homologous with the seta of mosses has been questioned, but no alternative evolutionary model has hitherto been proposed. Ligrone et al. explore the origin of the sporophyte shoot in terms of changes in embryo organization, within the framework of molecular phylogeny placing the three bryophyte lineages at the base of the phylogenetic tree of land plants, and using stomatal distribution as a guideline. They interpret the sporophyte shoot as a sterilized, indeterminate sporangial axis interpolated between the embryo and the fertile sporangium. The model proposed fills the gap between bryophytic and non-bryophytic extant land plants and offers clues for prospective evo-devo research.