Root nodules and (lateral) roots are hypothesized to share common developmental programs. Root development is the result of superimposed programs that take place along two imaginary axes; the apical‐basal axis and the radial axis. Recently, it has been shown that PLETHORA genes that initially in Arabidopsis thaliana had been shown to be essential for root apical‐basal patterning are also needed for proper nodule development in Medicago truncatula. PLETHORA genes act in parallel with the radial patterning module consisting of SHORT‐ROOT and SCARECROW genes. However, whether the orthologs of these genes are also involved in nodule formation remains unclear. To this end we studied the activation pattern of M. truncatula SHORT‐ROOT and SCARECROW by in situ hybridization. These studies revealed that both genes show an overlapping expression pattern in the nodule central meristem, and a mutual excluding expression pattern in the nodule vasculature. Further studies show that the activity pattern of the promoters of the A. thaliana SHORT‐ROOT and SCARECROW genes in the M. truncatula root is similar to that in A. thaliana roots. In the nodule the activity is confined to tissues of the nodule vascular bundle. We hypothesize that MtSHR and MtSCR in the nodule central meristem and nodule vascular bundle control different developmental programs.