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This study focused on bio-guided isolation based on antioxidant activities from Dicranopteris linearis spores and Averrhoa bilimbi branches. The total phenolic content (TPC), total flavonoid content (TFC), and antioxidant activities of the extracts were determined. For D. linearis spores, the ethyl acetate (EA) extract exhibited the highest TPC (120.13 ± 0.04 mg GAE/g) and TFC (21.94 ± 0.30 mg QE/g), along with strong DPPH antioxidant activity (96.3 ± 0.3% inhibition, IC50 of 39.4 ± 0.3 µg/mL). For A. bilimbi branches, the n-hexane–ethyl acetate (HEA) extract showed the highest TPC (165.21 ± 0.24 mg GAE/g) and TFC (26.20 ± 0.01 mg QE/g), with significant DPPH antioxidant activity (89.6 ± 0.7% inhibition, IC50 of 39.7 ± 1.9 µg/mL). Phytochemical investigation led to the identification of ten compounds (D1–D10) from D. linearis spores and twelve compounds (A1–A12) from A. bilimbi branches. Notably, compound A1 was identified as a new natural compound. The chemical structures were elucidated through NMR spectroscopy and comparison with existing literature. The antioxidant activities of selected compounds (D3–D5, D8–D10, and A1–A11) were evaluated using DPPH and ABTS free radical scavenging assays. Among them, compound A3 exhibited the strongest antioxidant activities (IC50 of 7.1 ± 0.1 µg/mL for DPPH and 14.8 ± 0.1 for ABTS, respectively). The results of this study highlight the potential of D. linearis and A. bilimbi for use in natural product-based antioxidant applications.