Stomata complexes are epidermal specialized structures typical of the upper aerial part of plants (shoot). In the model plant Arabidopsis thaliana, we show that in the hypocotyl (the) junction between the shoot and the root), stomata are organized according to a clear pattern reminiscent of the root epidermis pattern. Although stomata complexes are typical of the shoot epidermis, their pattern on the hypocotyl is under the control of genes involved in root epidermis patterning. Moreover, we have isolated a GFP marker line for the hypocotyl epidermal cells which do not differentiate stomata complexes. In this line the root and the hypocotyl epidermal patterns are similar. Our data support the existence of interactions between developmental mechanisms involved in the control of the apical/basal polarity and the radial symmetry of the plant body.