Two new anthraquinones, (11S)-1,4,6-trihydroxy-7-(1-hydroxyethyl)-3-methoxyanthracene-9,10-dione (1) and (11S)-1,6-dihydroxy-7-(1-hydroxyethyl)-3-methoxyanthracene-9,10-dione (2), together with six known compounds, including four naphthoquinones (3–6), one thiophene derivative (7), and one cyclohexanedione derivative (8), were isolated from the mangrove rhizosphere soil-derived fungus Fusarium sp. J3-2. Compound 1 displayed weak to moderate antibacterial activities against five strains of pathogenic bacteria with MIC values ranging from 25 to 50 μg/mL. Compound 3 showed weak cytotoxic activities toward human hepatocellular carcinoma cell lines, SMMC-7721 and SGC-7901, with IC50 values of 48.87 and 41.23 μg/mL, respectively. Compounds 1–7 exhibited antifouling activities against the larval settlement of the barnacle Balanus amphitrite.