Fruit rot caused by Aspergillus niger and Colletotrichum sp. could cause rapid and severe damage on orange fruits. Current control method of orange fruits is mainly applied by usage of harmful pesticides, leading to chemical residues on fruits, environmental pollution and human poisoning. One of alternative methods of reducing pesticides is to use botanical extracts. This study was conducted to evaluate the in vivo antifungal efficacy of aqueous extracts from the leaves of neem and basket plants against A. niger and Colletotrichum sp. Orange fruits artificially inoculated by fruit rot pathogens were immersed into leaf extracts of 6% (w/v) neem or basket plants for 30 s, and kept for 11 days to record lesion length at room temperature. Orange fruits immersed into sterile distilled water were used as the control treatment. The results showed that at 11 days after inoculation, extracts of neem and basket plants significantly reduced the Aspergillus rot lesions by 109.08 and 124.00 mm, respectively. In addition, anthracnose lesions on orange fruits were statistically inhibited by treatments of neem and basket plants, with the average lesion diameters approximately 160.00 and 154.75 mm, respectively, at day 11 of the conducting experiment. The results of this study showed that leaf extracts of neem and basket plant at the concentration of 6% could be used as a natural alternative to control the in vivogrowth of rot pathogens of orange fruits. These extracts have a bright future in modern plant protection to replace conventional synthetic pesticides in agro-ecosystem.