While sex determination is a fundamental process in vertebrate development, it is very plastic. Diverse genes became major sex determinants in teleost fishes. Deciphering how individual sex-determining genes orchestrate sex determination can reveal new actors in sexual development. Here, we demonstrate that the Y-chromosomal copy of the TGF-β family member gdf6 (gdf6Y) in Nothobranchius furzeri, an emerging model organism in aging research, gained the function of the male sex determinant through allelic diversification. To this end, gdf6Y is expressed by a subset of Sertoli-like cells. This eventually leads to the suppression of the onset of oogenesis in N. furzeri’s early sexual development, which itself is driven by the feminizing piscine germ cell factor foxl2l. Furthermore, we have identified downstream effectors of Gdf6Y. Besides TGF-β signaling modulators, especially the inhibitor of DNA binding genes id1/2/3, we found the mRNA decay activator zfp36l2 as a new TGF-β signaling target.