Fungicides are generally used for increasing the yield of the crop but they can induce harmful changes in seed germination and also seedling growth. Therefore, the present study was carried out to evaluate the effect of Difenoconazole and Azoxystrobin as fungicides on the germination of monocotyledonous seed (wheat; Triticum aestivum L.), and dicotyledonous seeds (radish; Raphanus sativus), then effect on Tomato (Solanum lycopersicum L.) seedling growth. Seeds of wheat and radish and seedling of tomato were treated with different concentrations of the tested fungicides; recommended, half and the double recommended dose compared with the untreated control. The results showed that the two tested fungicides significantly decreased seed germination%, root and shoot length of both wheat and radish seeds at the different applied doses compared to the control. The highly significant reduction in relative root and shoot length% and the relative germination% of wheat and radish seeds were observed when exposed to Difenoconazole or Azoxystrobin in which double recommended doses being 23.20, 27.88, and 43% or 13.20, 26.02, and 30.10% in wheat seeds, however, the reduction were 22.30, 37.69, and 63.0% or 17.67, 51.67, and 40.70% in radish seeds, respectively. In the case of tomato seedlings; carotene, chlorophyll a, chlorophyll b and total chlorophyll were significantly decreased after three weeks from both fungicides application by the double recommended doses, which recorded 0.04, 2.25, 0.15, 2.40 mg/g fresh weight for difenoconazole or 0.06, 1.66, 0.39, 2.05 mg/g fresh weight for azoxystrobin, respectively. Because Difenoconazole is less hazardous than Azoxystrobin, it might be advised that wheat and radish seeds be treated with it before sowing. Three weeks after being exposed to the fungicides, tomato plants treated with Azoxystrobin displayed a decrease in the a/b ratio at the indicated dose.