Chitosan is found in the cell structure of Zygomycetes fungi. It is a deacetylated chitin derivative, nature's second most abundant polysaccharide after cellulose. The current proposal used antimicrobial fungal chitosan polymer substances against foodborne bacterial pathogens. Ten fungal isolates were isolated from soil in the present investigation, and chitin was extracted from the fungal cell wall to produce chitosan. These isolates belonged to the Rhizopus, Aspergillus, Trichoderma, and Penicillium genera. Rhizopus sp. code RL was the most effective isolate regarding mycelium dry weight (1.05g/L) and chitin and chitosan yields (0.86 g/g mycelium and 0.12 g/g chitin). The chitosan productivity and yield coefficients relative to mycelium dry weight were 0.03 g/L/d and 0.11 g/g/L, respectively. 18S rRNA sequencing-based phylogenetic analysis revealed that this isolate had a 100% similarity to Rhizopus arrhizus for molecular identification. The gene sequences identified during the current study have been submitted to the GenBank database under the accession number OR398886. The fungal chitosan polymer chemical structure was identified using 1H nuclear magnetic resonance. In addition, the tested polymer was used as a natural antibacterial agent against foodborne pathogenic bacterial strains. The results showed that Staphylococcus aureus As4 and Salmonella typhimurium As3 were more susceptible to the fungal polymer, with inhibition zones measuring 24 and 15 mm and minimum inhibitory concentrations of 2.5 and 1.25 mg/mL, respectively. The tested polymer did not exhibit any cytotoxicity in the cell line with IC50 of 367.49±7.16 µg/mL. In order to preserve food in the future, Rhizopus arrhizus RL chitosan polymer will be used as a green-friendly polymer.