To study the coexistence of sexual and gynogenetic forms, we examined the population structure of a gynogenetic complex of the Japanese crucian carp, Carassius auratus Temminck et Schlegel, during the April--June reproductive season by collecting 1225 mature fish that migrated from Lake Suwa to a tributary river for spawning. There were more sexual fish (about 80%) than gynogenetic fish in this complex, and the operational sex ratio in the sexual form was female biased (males were about 20%). Mean standard length and body weight of sexual females were larger than those of sexual males. Sex ratio was male biased in smaller fish (standard length, <8.5 cm) but female biased in larger fish (standard length, ≥8.5 cm). We determined age by scale ring marks; the average age of sexual females was higher than that of males, but there was no significant difference in the average age between sexual and gynogenetic females. Sex ratio in the sexual form was more female biased for old than for young fish, and the mean size of sexual females was larger than that of males of the same age. The clear female-biased sex ratio and age difference between sexual females and males can be explained either by (1) higher mortality of males or by (2) female-biased sex allocation. The latter process reduces the disadvantage of sex and contributes to the coexistence of sexual and gynogenetic forms.