Abstract: Effects of physical seed sorting, seed treatment with garlic extract (1:2) and Vitavax 200 (0.4%) were investigated for controlling seed borne fungal flora and seed yield of jute (Corchorus capsularis L.). Seed health test of jute revealed that farmer`s saved seed (control) yielded all together 13 different fungi of 11 genera. Prevalence of Colletotrichum corchori, Macrophomina phaseolina, Botryodiplodia theobromae, Fusarium spp., Penicillium spp., Aspergillus niger and A. flavus were by 4.25, 10.75, 2.00, 4.25, 27.20, 8.00 and 22.50%, respectively. Septonema secedens Corda. was recorded as seed borne for the first time in jute. Garlic extract and Vitavax 200 increased the yield of jute by 47.38% and 46.05%, respectively over farmer`s saved seed (control) when grown in the net house. Under field conditions seed treatment with garlic extract and Vitavax 200 increased seed yield by 77.50 and 82.50%, respectively over farmer`s saved seed.