White campion (Silene latifolia) is a dioecious plant male heterogamety and large distinct X and Y sex chromosomes. The Y-chromosome contains two sex-determining factors: Stamen Promoting Factor (SPF) and Gynoecium Suppression Factor (GSF). We identified and analysed the sex-determining GSF gene in S. latifolia (GSFY) as well as its X-linked paralog GSFX. GSFY was found to be a Y-linked ortholog of CLAVATA3 (CLV3), which encodes a peptide with 12 amino acid residues regulating the size of shoot apical meristem (SAM) and carpel. RT-PCR results showed that GSFY is expressed in the SAM and early male flower buds, while GSFX is expressed in both male and female SAMs. In situ hybridization showed GSFY expression in gynoecium primordium in the male flower buds. When GSFY was introduced into Arabidopsis thaliana, it suppressed carpel development, unlike GSFX, which had no effect. The treatment with GSFY peptide led to a reduction in the sizes of shoot apical meristems (SAM) in both A. thaliana and S. latifolia. However, the application of GSFX peptide did not influence the SAM sizes. These results suggest the evolution of dioecy in S. latifolia may involve not only the active GSFY gene on the Y chromosome but also GSFX dysfunctionalization on the X chromosome, creating a male-specific mechanism to suppress gynoecium development. This insight sheds light on the genetic underpinnings of plant sex differentiation and evolution.