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A questionnaire-based survey on rice farmers’ source of seeds, cultivar planted, storage conditions and practices employed in the storage of rice seeds and pests and diseases encountered in storage was conducted in three selected rice-growing districts of Ashanti Region, Ghana. Seedborne fungi associated with farmer-saved rice seeds were assessed. Again, the efficacy of ginger rhizome, lemon grass and chili pepper aqueous extracts (100% w/v), and Mancozeb (check) were evaluated against seven seed-borne fungal species of rice in-vitro. Sixty seed samples collected from the interviewed farmers were examined for the presence of seed-borne fungi using the blotter method. Seed sample with high incidence of fungal pathogens selected after seed health test was soaked separately in the aqueous extracts, Mancozeb and water for 24 h. The seeds were later plated on blotter papers in Petri dishes. From the survey, majority of smallholder rice farmers interviewed (71.7%) saved their own seeds for planting and only 18.4% of the farmers treated their seeds during storage and before sowing. Twenty seed-borne fungal species were recovered from the rice seed samples from the three districts, the major pathogenic ones including Bipolaris oryzae, Fusarium spp., Colletotrichum sp., Curvularia spp. and Cercospora sp. Soaking the seeds in aqueous lemon grass extract (100% w/v) was effective in managing the seven seed-borne fungal species when compared with the other aqueous extracts.