Watermelon fruit that results from pollination with pollen irradiated with soft-X-ray contains only empty seed, although the fruit develops to a normal size. In this study the processes of fertilization and embryo formation were compared between unirradiated and irradiated pollen in order to reveal the mechanisms by which seedless fruits are generated. The use of soft-X-irradiated pollen resulted in normal pollen tube penetration into the synergid and discharge of sperm cells. Two to three days after pollination, the sperm nucleus was present alongside the egg nucleus before fusion. The polar nuclei divided and the endosperm cell spread in the embryo sac before zygote division. A globular embryo was observed on day 7 to 10 after pollination. Subsequently, the embryo failed to differentiate to organ tissue and degenerated. These results indicate that double fertilization occurred after pollination with the irradiated pollen and that abortion of the embryo results from soft-X-ray induced chromosomal abnormalities in generative nucleus.