Fungal diseases in fish cause economic losses all over the world, and knowledge about them is scarce and outdated in Aswan Governorate, Egypt, making interpretation, prevention, and treatment difficult. The necessity to find a fungicide that is natural, environmentally friendly, and does not emerge drug resistance is a must. Therefore, the current study aimed to isolate and diagnose fungal infection in farmed Oreochromis niloticus, causing mortalities, in Aswan Governorate. During 2021, 200 fresh O. niloticus samples were collected from the Sahary Fish Hatchery and Aswan General Authority for Fish Resources Development fish farm. Some fish showed hemorrhagic lesions all over the body, detachment of scales, and fin erosion. Collected tissue samples were cultured on potato dextrose agar and Sabouraud dextrose agar for phenotypic characterization. Macroscopic and microscopic analyses were used to identify the isolated fungi. A total of 18 fungal species and two varieties appertaining to ten fungal genera were recovered from 48 samples out of 200 examined O. niloticus (24%), with Aspergillus flavus being the most prevalent at a rate of 25.6%. The isolated A. flavus was proven to be pathogenic to farmed O. niloticus, as by experimental infection. The natural herb Persicaria salicifolia had an LC50 value of 41.68 mg/l in exposed O. niloticus and was used to treat A. flavus-infected O. niloticus. It can be concluded that A. flavus poses a major hazard to O. niloticus aquaculture and can be treated with 40 mg/kg in feed or 20 mg/l in water of P. salicifolia for 6 days.