Flower color polymorphism exhibited by natural populations provides an opportunity for understanding the evolutionary mechanisms contributing to the diversity of floral morphology. However, little is known about the color polymorphism of female organs in flowering plants. Here we report gynoecium color polymorphism in Butomus umbellatus (Butomaceae), an emergent, aquatic monocot. Populations from Mishan, northeastern China comprised two morphs; gynoecia are either pink, as observed in other areas, or white. We measured floral traits and female fecundity in the two gynoecium color morphs in the field. There was no significant difference in plant height, pedicel length, and flower size including petal, sepal and gynoecium between the two morphs, but plants with pink gynoecia had wider inflorescence stalks, larger inner whorl anthers and produced more pollen and ovules than those with white gynoecia. Correspondingly, we found that seed production was significantly higher in the pink than in the white morph. This new finding suggested selection against white gynoecia in part because of low fecundity, consistent with the rarity of the white gynoecium morph in this species.