Endophytic fungi are identified as mitosporic and meiosporic ascomycetes that asymptomatically inhabit the internal tissues of some plants. They have a beneficial role in plant protection as more as producing several natural bioactive products. So, the present study aimed to isolate endophytic fungal species which associated with roots of tomato plants, sub-cultured in pure cultures and identified them according to their morphological and genetics characterization. The results introduced seven fungal species belong to the genera Alternaria, Aspergillus, Penicillium, Talaromyces and Triangularia which identified according to their cultural appearance and microscopic examination features. Their identification was confirmed by molecular characterization using sequencing the ITS and β-tubulin genes then deposited in GenBank with an accession numbers serial from OP599904.1 to OP599910.1 for ITS and from LC733668 to LC733674 for β-tubulin. Additionally, the antioxidant, antibacterial and antitumor studies of the crude filtrates of the isolated endophytic fungi revealed high antioxidant potential, negative antibacterial and successful antitumor activities.