The functional unit for gas exchange between plants and the atmosphere is the stomatal complex, an epidermal structure composed of two guard cells, which delimit a stomatal pore, and their subsidiary cells. In the present work, we define the basic structural unit formed in Arabidopsis thaliana during leaf development, the anisocytic stomatal complex. We perform a cell lineage analysis by transposon excision founding that at least a small percentage of stomatal complexes are unequivocally non‐clonal. We also describe the three‐dimensional pattern of stomata in the Arabidopsis leaf. In the epidermal plane, subsidiary cells of most stomatal complexes contact the subsidiary cells of immediately adjacent complexes. This minimal distance between stomatal complexes allows each stoma to be circled by a full complement of subsidiary cells, with which guard cells can exchange water and ions in order to open or to close the pore. In the radial plane, stomata (and their precursors, the meristemoids) are located at the junctions of several mesophyll cells. This meristemoid patterning may be a consequence of signals that operate along the radial axis of the leaf, which establish meristemoid differentiation precisely at these places. Since stomatal development is basipetal, these radially propagated signals may be transmitted in the axial direction, thus guiding stomatal development through the basal end of the leaf.