With the first approval of a genetically modified (GM) soybean for uncontained use in Japan, information about hybrids of wild and GM or non-GM soybeans has become increasingly important. Therefore, we generated and characterized various hybrids between wild and GM or non-GM soybeans in a containment greenhouse, and investigated the inheritance of the cp4 epsps transgene and its effects on the hybrids. The hybrids inherited the cp4 epsps gene in a Mendelian fashion. The gene was stably expressed and produced functional protein, conferring glyphosate tolerance to the hybrids. We also examined the germination and survival rates of the second filial (F 2 ) seeds and those of hybrids backcrossed twice (BC2F 2 ) after a 3-month treatment at 4°C. Hybrids displayed similar germination characteristics as wild soybean after cold treatment. The majority of the BC2F 2 seeds survived as dormant seeds. There was no effect of the cp4 epsps gene on the survival rate. Furthermore, we examined the morphology, anthesis, and fecundity of the hybrids. On the whole, the F 1 , F 2 , and F 3 hybrids exhibited morphology, anthesis, and fecundity phenotypes that were intermediate between wild and cultivated soybeans; those of BC2F 2 hybrids were similar to those of wild soybean. Comparisons between GM and the corresponding non-GM hybrids did not reveal significant differences in fecundity. We suggest that hybrids containing half of their genes from wild soybean and half from cultivated soybean display fitness that are intermediate between wild and cultivated soybeans, whereas BC2F 2 hybrids have fitness similar to that of wild soybean. We also suggest that, despite being stably inherited, the cp4 epsps gene does not affect fitness in the absence of glyphosate treatment.