The Japanese flounder () is an economically important marine fish that has been widely cultured in Japan, Korea, and China. The growth rate of females is significantly higher than that of males; production of all-female Japanese flounder populations for aquaculture has considerable advantages for improving yield and economic benefit. Gynogenesis is a type of parthenogenesis whereby homologous or heterologous sperms penetrate into the eggs and trigger embryogenesis; however, the sperm nucleus does not fuse with an egg nucleus to form a zygote. Thus, gynogenetic individuals inherit only maternal genetic information. In this review, we introduce the recent progresses of artificial introduction of gynogenesis in Japanese flounder. First, we describe the methods of meiogynogesis and mitogynogenesis. Next, we review the applications of gynogenesis in Japanese flounder, such as sex control and production of clones. Finally, we propose a breeding system using gynogenesis and discuss its potential applications in the genetic improvement and breeding of new variations in fish.