This research was performed to provide germination characteristics of environmental risk assessment for genetically modified (GM) CMV-resistant pepper. For the germination test, a CMV-resistant GM line (H-15), its non-GM parental line (P-2377), and two non-GM cultivars ('Shingang' and 'Manita') were used. The germination of all tested lines was maintained by immersing fully matured red peppers for 60 days in a 200L container where fresh underground water was constantly supplied. The fresh peppers and seeds were placed into plastic bags filled with 3 times the amount of distilled water compared to the volume of peppers and seeds and incubated at 10, 20 and 30°C for 3 months. The germination of pepper fruits from the 4 lines was maintained for 2 months as at 10 and 20°C, but for only 1 month at 30°C. In addition, the germination of seeds from the 4 lines was maintained over 85% for 3 months at 10 and 20°C and 2 months at 30°C. A wintering test was also conducted at the farm water reservoir (7 × 7 × 1.5 m) over 2 years. The germination of the 'Manita' line was maintained for only 6 to 7 months and that for the other 3 lines for 7 to 8 months. It was found that the pepper seeds were geminated in the water in June (storage period: 7 months) over 20°C of water temperature. 'Shingang' lines with a strong spiciness had the highest germination rate, while 'Manita' with low spiciness had the lowest germination rate. H-15 and P-2377 with a moderate germination rate showed no significant difference between them. Since GM peppers in water germinate well for 2 months in autumn and 6 to 8 months in winter, it is important to carefully manage the peppers produced from GM farms to prevent ecological disturbance from storms, heavy rains, and other factors.