During anther development a series of cell specification events establishes the male gametophyte and the surrounding sporophytic structure. Here we show that the homeobox gene WUSCHEL, originally identified as a central regulator of stem cell maintenance, plays an important role in cell type specification during male organogenesis. WUS expression is initiated very early during anther development in the precursor cells of the stomium and terminates just before the stomium cells enter terminal differentiation. At this stage the stomium cells and the neighboring septum cells that separate the pollen sacs undergo typical cell wall thickening and degenerate which leads to rupture of the anther and pollen release. In wus mutants, neither stomium cells nor septum cells differentiate or undergo cell death and degenerate. As a consequence, the anther stays intact and pollen is not released. CLAVATA3 which is activated by WUS in stem cell maintenance, is not activated in anthers indicating a novel pathway regulated by WUS. Comparing WUS function in stem cell maintenance and sexual organ development suggests that WUS expressing cells represent a conserved signaling module that regulates behavior and communication of undifferentiated cells.