Grain samples of 14 Egyptian wheat cultivars were tested for seed-borne fungi. The deep freezing method was used. Five seed-borne fungi viz., Aspergillus flavus, A. niger, Curvularia lunata, Fusarium moniliforme and Penicillium chrysogenum were isolated from the wheat cultivars viz., Bani Suef 4, Bani Suef 5, Gemmiza 7, Gemmiza 9, Gemmiza 10, Giza 168, Misr 1, Misr 2, Sakha 93, Sakha 94, Shandaweel 1, Sids 1, Sids 2 and Sids 3. A. flavus, A. niger and F. moniliforme were the most prevalent fungal species. Their incidence ranged from 21.0–53.5%, 16.0–37.5%, and 12.0–31.0%, respectively. The antifungal potential of water extracts from aerial parts of five wild medicinal plants (Asclepias sinaica, Farsetia aegyptia, Hypericum sinaicum, Phagnalon sinaicum, and Salvia aegyptiaca) were collected from the Sinai Peninsula, Egypt. The antifungal potential of water extracts from the aerial parts of these five plants were tested in the laboratory against the dominant fungi isolated from the wheat cultivars. All the aqueous plant extracts significantly (p ≤ 0.05) reduced the incidence of the tested seed-borne fungi. But the extract of Asclepias sinaica exhibited the most antifungal activity on tested fungi at all concentrations used when compared with other plant extracts. Maximum infested grain germination was observed in Giza 168 and minimum in Bani Suef 5. Treating grains with plant extract of A. sinaica (10%) enhanced the percentage of grain germination of all cultivars in both laboratory and pot experiments. Maximum root and shoot length of seedlings was recorded in Bani Suef 4 during fungal infestation or treatment by plant extract. For one hour before sowing or storage, the aqueous extract of A. sinaica can be used to treat wheat grains, to reduce the fungal incidence. Aqueous extracts of the aerial parts of selected medicinal plants, particularly A. sinaica, are promising for protecting Egyptian wheat grain cultivars against major seed-borne fungi. The aqueous extracts are expected to improve crops.