Egypt imported different cultivars of tomato seeds from different companies. Different microorganisms associated these seeds, among them the seed borne fungi. Seeds of five different companies were collected and subjected to fungal isolation using Standard blotter Technique and agar plate technique. Results revealed that five species were observed. The observed fungi were morphologically identified under microscope and the results were confirmed using specific PCR with primers (ITS-1 & ITS-4). Amplicones with molecular size 600 bp was observed. The bands were purified and subjected to DNA sequence. The sequence analysis revealed that the five fungi are Trichoderma longibrachiatum, Aspergillus fumigatus, A. fumigatus strain TFR-8, A. flavus and A. oryzae. The sequences were submitted into the Gene Bank and were deposited under accession no. KJ424352, KJ424353, KJ734707, KJ734708 and KJ742820. T. longibrachiatum was used as biocontrol agent against several plant pathogenic fungi and the results showed significant growth inhibition for the treated fungi with percentage ranging from (49.7 % to 73.4%). Using T. longibrachiatum strain as abiological control agent is effective, applicable, safe and commercial.