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Sagittaria species have been reported to display remarkable variation in gender expression. Here, we investigated gender variation in Sagittaria pygmaea, the smallest sized monoecious species in the genus. We used the midvein length as an indicator of plant size and production of male and female flowers as an indicator of gender variation in a single inflorescence. We counted the total number of inflorescences to assess the effect of inflorescence variation on the gender variation pattern. Our results showed that variation in inflorescence number did not affect gender variation. Male flower production increased with increasing plant size, but female flower production did not. Plants of S. pygmaea might enhance their paternal reproductive success by increasing the number of male flowers with increasing plant size.