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Disease-Resistant Habanero Yellow Hot Chilli Seeds For Planting. Chilli pepper seeds can sow in any season (throughout the year) but thrive in warm and humid conditions. Generally, chili pepper seeds are sown in a seedling tray and then transplanted after the seeds germinate. transplant is necessary because it allows the plant to grow freely. The best temperature for chili seed germination is between 15-32°C.Take a seedling tray, fill the seedling tray with a growing medium, and spread the chilli seeds on it, then cover a thin layer of soil above the seeds. Give light water through a watering sprayer. Keep the chilli seedling tray in a sunny spot and keep the soil moist. Chilli Seeds will germinate within 6-10 days.