The microorganisms use as the biological control of plant pathogens have the ability to biosynthesize nanoparticles such as nano-selenium which have applied in various fields, including agriculture. Biosynthesis selenium nanoparticles (SeNPs) is done by some bio-agents i.e. Trichoderma harzianum, Chaetomium globosum, Streptomyces griseus, Pseudomonas putida and Bacillus subtilis and evaluated their fungicidal activities against soil-borne diseases in fennel plants (Foeniculum vulgare L.) caused by Macrophomina phaseolina, Fusarium solani, and fungus like Pythium aphanidermatum. In vitro experiments, all tested treatments were significantly reduced growth of pathogenic fungi i.e. M. phaseolina, F. solani and P. aphanidermatum as compared with untreated control. Morover, under greenhouse conditions, results indicated that all tested treatments were significantly reduced damping-off and root-rot diseases of fennel plants. SeNPs synthesis by S. gresius were the higher effect than other treatments. Also these treatments were found to increase the activity of oxidative enzymes i.e. peroxidase, polyphenoloxidase, chitinase and soluble proteins. Furthermore, under field conditions, fennel seeds treated with the selected SeNPs synthesis by bioagents at a concentration of 250 ppm were affected to reduce damping-off and root-rot diseases of fennel plants. The commercial biocide (Bacillus subtilis) was also used in the same manner. A concentration of 0.5 ml/L was applied for comparison and the untreated seeds were used as control treatment. Results indicated that SeNPs synthesis of S. griseus showed the most effective treatment. They showed the highest increase in all growth parameters / plant i.e. plant height, number of branches, dry weight of inflorescences, dry weight of seeds, dry weight of 1000 seeds, plant yield, percentage of volatile oil and its frequency during the two successive growing seasons.