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One hundred wheat (Triticum aestivum L.) accessions were selected on the basis of different geographical areas of Pakistan. Isolation and identification of seed born fungi were conducted according to standard blotter test and a total of five major seed borne fungi including Alternaria alternata, Aspergillus niger, Fusarium species, Drechslera species and Phytophthora species were isolated from the wheat seeds. The frequency of occurrence of these five seed born fungi was 49, 46, 42, 35, and 16%, respectively. Infection percentage varied from 0 to 90% in all 100 wheat accessions. Among the accessions, the highest infection (100%) of seed born fungi was recorded in 011185 and 011757 accessions while the lowest infection (10%) was recorded in 011415 accessions. Moreover, in accessions collected from Gilgit Baltistan and Azad Jammu Kashmir. Alternaria niger and Alternaria fusarium were dominant, while in Khyber Pakhtunkhawa province, A. niger was prevalent followed by A. alternata. In the case of Baluchistan province, the dominant seed born fungi was A. alternata followed by Drechslera spp. Similarly, in case of Punjab, the occurrence of A. alternata, Drechslera spp., Fusarium spp., and A. niger associated with seeds were similar. For accession collected from Sindh province, the dominant seed born fungi was A. niger and Drechslera spp. However, the Phytophthora spp. infection of wheat seeds accession of Baluchistan was the highest followed by wheat seeds accession collected from Gilgit Baltistan and AJK, Kpk and Punjab, whereas wheat seeds accessions collected from Sindh province were found to be free from Phytophthora spp.