The Study aims to evaluate the effectiveness of various treatments against Geotrichum citri-aurantii and Alternaria citri in vitro. Samples were collected from three governorates: Beheira, Qalyubia, and Sharqiah. Qalyubia showing the highest frequency of Geotrichum sp. and Fusarium sp., while Alternaria sp. was the most prevalent in all governorates. The molecular identification of G. citri-aurantii and A. citri offers valuable insights into the genetic makeup and diversity of fungal pathogens affecting Navel Orange fruits. By sequencing the ITS1 and 5.8S ribosomal RNA regions, the study successfully identified both species with high genetic similarity to known strains. Phylogenetic analyses further revealed genetic clustering, indicating some degree of diversity within these species. A range of biotic and abiotic treatments were tested, including bio-agents like Trichoderma viride and Bacillus amyloliquefaciens, essential oils i.e., clove, thyme and ginger oils and chitosan and chitosan nanoparticles (NPs). Results showed that essential oils had varying inhibitory effects on fungal growth while chitosan and chitosan nanoparticles (NPs) were highly effective in reducing growth. Most notably, chitosan (NPs) showing highly effectiveness at lower concentrations. Additionally, Trichoderma viride was more effective than B. amyloliquefaciens in reducing the liner growth of G. citri-aurantii and A. citri.