Abstract: Seed of 10 sesame (Sesamum indicum L.) cultivar supplied by National Agriculture Research Center, Islamabad were tested for seed borne mycoflora by standard blotter paper test. 11 phytopathogenic fungi viz., Alternaria brassicola, A. redicina, Aspergillus alba, A. flavus, A. niger, A. viridus, Cephalosporium sp., Curvularia sp., Drechslera sp., Fusarium sp. and Penicilliu, sp. were found associated with these samples. Percentage of seed sample infection and extent of fungal infection ranged from 0.75-53%. The effect of associated fungi on germination capacity was evaluated by the standard rolled paper towel method. The associated fungi decreased the germination potential. 11 fungi were isolated from abnormal seedling and ungerminated seeds.