The present study was carried out to isolate mycoflora linked with Chitra variety of sunflower seeds employed by agar and blotter paper methods. A total of 12 seed borne fungal species including Aspergillus flavus, A. fumigatus and A. niger, Alternaria alternata , A. helianthi, Curvularia lunata, Fusarium solani, Fusarium moniliforme, Macrophomina phaseolina, Mucor recemosus, Penicillium citrinum and Rhizopus nigricons were detected. There by germination was found to be reduced by 12-25%. Two systemic fungicides viz., Topsin and Bayleton were found to be significantly effective in the elimination of seed-borne fungi. Among the fungicides, best antifungal activity was achieved by Bayleton followed by Topsin and other fungicides show moderate efficiency on seed borne mycoflra on sunflower. During the evaluation of efficiency of bio agents Tricoderma harzianum was found to be most effective against Aspergillus niger and Alternaria helianthi and Trichoderma viride was most effective against Alternaria alternata and Curvularia lunata . Similarly that of Pseudomonas fluorescens was against Macrophomina phaseolina.