Desert ephemeral plants showcase a rapid life strategy, requiring quick and effective germination in the brief periods of favorable environmental conditions. We explored how Alyssum linifolium, a desert ephemeral with seed mucilage, repaired seed DNA under the genomic stress of desert conditions. We combined γ-irradiation-induced DNA damage with in situ dew treatments to simulate natural hydration process in the desert. We found that the mucilage layer significantly enhanced water absorption during dew formation and maintained hydration after sunrise, which provided a conducive environment for DNA repair. Over a 96-h dew exposure, irradiated seeds with intact mucilage, especially those with moderate damage, showed a notable decrease in DNA damage and a higher DNA repair rate compared to seeds without mucilage. Following the dew treatment, we noted an increase in germination percentage and a decrease in nonviable seeds, underscoring the vital role of mucilage in preserving genetic integrity and ensuring successful germination. This mucilage-facilitated repair mechanism is essential for A. linifolium, promoting DNA repair in seed cells and maintaining a viable soil seed bank. The study sheds light on the importance of mucilage for environmental stress of ephemeral plants inhabiting desert ecosystems.