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Watermelon seed being an oily seed is prone to rapid deterioration of its quality, hence maintaining quality during storage is germane. The study therefore investigated the effect of crude plant powder, storage containers and storage duration on the seed quality of two varieties of watermelon seeds. Seed lots each of 100 g of each variety were treated with 10 g of four crude plant powders of clove basil leaf, red chilli pepper fruit, garlic, neem leaf and a synthetic fungicide. All samples were stored in three storage containers (envelope, tin and glass bottle). Treated seeds were stored under ambient conditions for 180 days. Germination and seedling vigour were determined at 180 day time course after storage. Data were subjected to mean separation using Duncan’s Multiple Range Test. Significant differences were observed in the quality traits examined in water melon due to differences in variety, seed treatment, storage container and storage period. ‘Kaolak’ was the best in storage in terms of seedling vigour and viability. Glass bottle was identified as the best storage container in maintaining seed quality of water melon throughout the storage period. The use of organic materials especially neem and clove basil leaf powder proved much better for maintaining germinability and seedling vigour and extension of seed longevity than inorganic material.