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Numerous strategies have been suggested to reduce dependence on synthetic products, such as physical, microbial, and natural methods. Among the natural remedies, plant extracts have emerged as a popular option owing to their eco-friendly character, ease of degradation, and harmless nature to humans. In our study, we used the acetone and hexane extracts of Rhaphiolepis indica fruit to combat two fungal pathogens that were isolated from infected bean plants and showed root rot symptoms. The two pathogens were confirmed to be pathogenic by pathogenicity assays conducted in vivo. The morphological and molecular identification by ITS-region sequencing revealed that the two isolates were Rhizoctonia solani and Fusarium solani, and they were assigned accession numbers OQ880457 and OQ820158, respectively. Our data showed that both hexane and acetone extracts caused a significant decrease in the linear growth of F. solani at all concentrations used (1%, 2%, and 3%), compared to the control. However, at a concentration of 3%, the hexane extract caused much greater inhibition than the acetone extract. For R. solani, the hexane extract, shows a significant inhibition percentage at all concentrations, which further increases to 85.24% at 3% concentration. The HPLC of both extracts indicated the presence and absence of phenolic and flavonoid compounds. The obtained results revealed that five acetonic phenolic extract compounds were ferulic, p-coumaric, gallic, p-OH benzoic, and cinnamic, with concentrations of 5.31, 10.36, 7.24, 6.08, and 0.89 mg/mL, respectively. On the other hand, the five hexanoic phenolic compounds were catechol, caffeic, chlorogenic, p-OH benzoic, and cinnamic acids, with concentrations of 3.66, 5.14, 0.69, 6.31, and 13.47 mg/mL, respectively. The identified acetonic flavonoid extract compounds, namely rutin, chrysin, quercetin, kaempferol, chrysoeriol, 7-OH flavone, and naringin, had respective concentrations of 5.36, 10.23, 4.32, 15.33, 1.06, 0.087, and 0.069 mg/mL, respectively. In contrast, it was observed that the seven hexanoic flavonoid extracts comprised of rutin, quercetin, kampferol, luteolin, chrysoeriol, 7-OH flavone, and catechin exhibited concentrations of 5.36, 7.15, 18.20, 6.04, 2.04, 10.24, and 13.43 mg/mL, respectively. The results of the study suggest that plant extracts may be a useful natural remedy for combating fungal pathogens and reducing dependence on synthetic products.