Three bio agents Trichoderma harziznum, T. viride and Pseudomonas fluorescens were evaluated for their antagonistic effect on seed borne fungi. The germination percentage and seedling parameters in chilli were evaluated in vitro condition. Seeds were coated with spore suspension of each strains of Trichoderma supplemented with 2% of starch (w/v) as an adhesive at the rate 5x105 conidia/ml and talc powder formulations of P. fluorescens (1x108) at the rate 5g/kg seed. All the antagonists reduced the seed mycoflora incidence, significantly increased seed germination, root and shoot length although the results varied with different bio agents treatments. The treated seeds were evaluated for reduction of Alternaria alternate, Curvularia lunata, Aspergillus niger, Aspergillus flavus, Rhizopus stolonifer. The study indicated that T. harziznum was more effective in reducing the seed associated fungi and proved to be superior for inhibition of the above pathogen as compare to T. viride and P. fluorescens. Less association of seed borne fungi was exhibited by pre-treated seed samples over untreated ones (control).