Mechanisms enabling the maintenance of sexual and apomictic modes of seed formation in sympatry are poorly understood. Dobeš et al. study populations of Potentilla puberula representing various combinations of five polyploid cytotypes (tetraploid–octoploid) and use a flow cytometric seed screen to calculate the male genomic contribution to the embryo and endosperm. They find a rare example of intraspecific differentiation into sexual and apomictic cytotypes at the polyploid level, with the integrity of sexual tetraploids being maintained due to reproductive isolation from the apomictic higher polyploids. The functionality of the gametophytic self-incompatibility system suggests that the tetraploids are functional diploids.