Post-harvest rot symptoms caused by complex airborne fungi are nowadays the most serious threatening disease affecting orange fruits in Nigeria and presumably in many African countries. Experimental trials were conducted at the Department of Biological Sciences (Akwa Ibom State, Nigeria) from January to December 2022 to ascertain the pathogens associated with postharvest fruit rot of oranges (Citrus aurantium L.). Results of the pathogenic test revealed that Fusarium sp. and Penicillium sp. are pathogenic and produced the highest lesion diameter (38.67 and 40.33 mm, respectively) and disease severity index (88.67 and 94.33%, respectively). The frequency occurrence of Fusarium sp. (69.14%) and Penicillium sp. (50.62%) was the highest. Two aqueous extracts of Azadirachta indica Juss. leaves and Zingiber officinale Roscoe rhizomes (at 80% concentration) were evaluated for their antifungal activities against the pathogenic isolates under in vitro and in vivo conditions. The results revealed that A. indica and Z. officinale aqueous extracts exhibited the highest mycelial growth inhibition (>90%) of Fusarium sp. and Penicillium sp. Similarly, under in vivo assay minimum lesion diameter (≤ 6.37 mm) and disease severity index (≤11.13%) were recorded in these aqueous extracts. In conclusion, the application of A. indica and Z. officinale can provide an alternative to fungicides against Penicillium sp. + Fusarium sp.