In the Brassicaceae, indehiscent fruits evolved from dehiscent fruits several times independently. Here we use closely related wild species of the genusLepidiumas a model system to analyse the underlying developmental genetic mechanisms in a candidate gene approach.ALCATRAZ(ALC),INDEHISCENT(IND),SHATTERPROOF1(SHP1) andSHATTERPROOF2(SHP2) are known fruit developmental genes ofA rabidopsis thalianathat are expressed in the fruit valve margin governing dehiscence zone formation. Comparative expression analysis by quantitative RT-PCR, Northern blot andin situhybridization show that their orthologues fromL epidium campestre(dehiscent fruits) are similarly expressed at valve margins. In sharp contrast, expression of the respective orthologues is abolished in the corresponding tissue of indehiscentL epidium appelianumfruits, indicating that changes in the genetic pathway identified inA. thalianacaused the transition from dehiscent to indehiscent fruits in the investigated species. As parallel mutations in different genes are quite unlikely, we conclude that the changes in gene expression patterns are probably caused by changes in upstream regulators ofALC, INDandSHP1/2, possible candidates fromA. thalianabeingFRUITFULL(FUL),REPLUMLESS(RPL) andAPETALA2(AP2). However, neither expression analyses nor functional tests in transgenic plants provided any evidence that theFULorRPLorthologues ofL epidiumwere involved in evolution of fruit indehiscence inL epidium.In contrast, stronger expression ofAP2in indehiscent compared to dehiscent fruits identifiesAP2as a candidate gene that deserves further investigation.