Arapaima gigas is a giant air-breathing and bony tongue fish from the Amazon basin and a promising species for aquaculture. A. gigas farming industry is still not established because of the lack of information on its reproductive physiology. Reproduction in captivity cannot be manipulated or stimulated, and the identification of males and females in a broodstock is not easy. We aimed to reveal the morphological sex differentiation of pirarucu as studies involving gonad development are essential to understanding the reproductive physiology of any species. We performed histological analysis on the whole body and extracted the gonads of 150 juveniles. The first sign of ovary differentiation is the sex-specific rearrangement of the germ cells. In 9 cm total length females, the germ cells group into nests and are restricted to the lateral face of the gonad, in close contact with the abdomen wall. With further development, this region invaginates and that later develops into ovigerous lamellae. Meiosis starts soon after ovary differentiation. In males, the germ cells are scattered along the elongated differentiating testis at first, and later become more restricted to the central region where the spermatogonial cysts start to develop. Somatic and germ cells are jointly involved in the cellular reorganization during gonadal differentiation, specifically when the germ cells begin to establish new associations during the development of both the germinal epithelium and stroma. RESEARCH HIGHLIGHTS: In Arapaima gigas, the ovary differentiation occurs in 9 cm TL females and it is marked by the rearrangement of germ and somatic cells; and the germ cells entering meiosis with no formation of ovarian cavity; testis differentiation occurs later and meiosis does not start in males smaller than 80 cm TL.