Annona muricata and Annona reticulata, known for their traditional medicinal uses and antimicrobial properties, were investigated for their potential antibacterial effects. Extracts from fresh leaves were tested for antimicrobial activity, revealing that Annona muricata exhibited superior antibacterial properties compared to Annona reticulata, especially against E. coli strains. In silico analysis focused on 46 phytochemicals extracted from Annona muricata, which were docked with key bacterial proteins, including Gyrase, the 30S and 50S ribosomal subunits, Topoisomerase IV, and penicillin-binding protein. Notably, phytochemicals such as Quercetin 3–O-rutinoside (Rutin), Quercetin 3-O-neohesperidoside, Quercetin 3-O-glucoside (Isoquercetin), Luteolin 3´7-di-O-glucoside, and Homoorientin demonstrated strong docking scores and confidence score, indicating potential interactions that could lead to bacterial destruction. These findings suggest that certain phytochemicals of Annona muricata is a promising candidate for antibiotic development, opening avenues for further exploration in combating bacterial infections.