Aspergillus and Fusarium species are the major seed-borne fungi occurring on onion in Burkina Faso according to a previous study. In order to work out effective, available and healthy method of seed treatment against these fungi, this study aimed to evaluate the antifungal activity of three local botanical species. Mycelial growth of Aspergillus niger, Fusarium moniliforme, Fusarium oxysporum and Fusarium solani was evaluated in vitro on media prepared with aqueous extracts of Cymbopogon citratus, Eclipta alba and Portulaca oleracea. The health and germination quality of seeds previously treated with the best aqueous extracts were then evaluated. The aqueous extract of C. citratus significantly inhibited the mycelial growth of all Fusarium species at rates ranged from 42,8 to 92,0% but stimulated the growth of A. niger. Those of P. oleracea inhibited the mycelial growth of all tested fungi at rates ranged from 3,2 to 42,4% while those of E. alba stimulated the mycelial growth of all tested fungi. Seed treatment with the extracts of C. citratus and P. oleracea allowed reducing their infection rates by fungi of over 50%. However, the emergence and growth of seedlings were respectively reduced by P. oleracea and C. citratus compared to those of untreated seeds. Our study concludes that both aqueous extracts have proven antifungal properties. The appropriated shape and dose of use, that does not affect the seedling emergence and growth, should be sought.