The phenotypic sex of many species of amphibians is subject to reversal by steroid hormones. The mechanism of this process, however, still remains largely unknown. As a step toward understanding the histological changes during sex reversal in amphibians, we analyzed two- and three-dimensional (2D and 3D) structures of sex-reversing gonads in Rana rugosa frogs. 2D views revealed that many oocytes in the wild-type ovary disappeared during female-to-male sex-reversal concomitant with the emergence of Vasa-positive small germ cells. Some of the germ cells were labeled with BrdU. BrdU-positive germ cells were few in the testosterone (T) treated ovaries at days 8 and 16, which resembled wild-type ovaries. Basement membranes became disrupted by day 24 in T-treated ovaries. However, the membranes were later reconfigured into testis-like gonadal structures 40 days after T treatment. 3D imaging of the sex-reversing gonad using serial immunostained sections showed that germ cells were organized in linear fashion extending out from where the sex-reversing gonad attached to the mesorchium 24 days after T treatment. Germ cells were increased in number by 40 days and were localized to the cortex of the gonads. In a T-untreated testis at day 24, many germ cells were distributed throughout the cortex except in the central space, while the efferent duct ran between two sheets of the mesorchium. These results, taken together, suggest that the mesorchium plays an important role in the organization of testicular structure. This is the first report showing germ cell ontogeny and organization in the female-to-male sex-reversing gonad in a vertebrate species.