The use of genetically modified (GM) crops has increased continuously over the world, and concerns about the potential risks of GM crops have also risen. Although, until now, GM crops have not been cultivated commercially in Korea, it is necessary to develop technology for the safe evaluation of GM crops. In this study, we investigated the influence of gene flow from GM to non-GM soybeans by the size of the pollen donor. In the experimental design, GM soybeans were placed in the center as a pollen donor and non-GM soybeans were placed in four directions as the pollen receivers. Three sizes of pollen donor were designed as 90 cm × 90 cm, 180 cm × 180 cm, and 360 cm × 360 cm. A total 22,719 seeds were collected from non-GM soybeans, and 14 hybrids were finally obtained through herbicide resistance screening and PCR analysis. The highest hybridization rate was 0.78% at a distance of 15 cm from a 360 cm × 360 cm GM pollen donor, and the farthest distance of hybridization was 180 cm from a GM pollen donor which was 360 cm × 360 cm in size. Ten hybrids were found among the 14 hybrids at the 360 cm × 360 cm pollen donor size, 3 hybrids at 180 cm × 180 cm, 1 hybrid at 90 cm × 90 cm. From these results, it could be concluded that with the larger pollen donor size, more hybridization occurred in soybeans.