Abstract:[Background] Naphthopyrones possess various bioactivities that are characteristic secondary metabolites of the fungus Aspergillus niger. [Objective] To illuminate the structures and activities of naphthopyrones from fungus A. niger isolated from mud flat. [Methods] Guided by TLC analysis, we used combined chromatographic and spectrographic techniques to identify naphthopyrones. The activities against pathogen bacteria and Artemia salina were tested by micro-dilution method. [Results] Six naphthopyrones: Rubrofusarin B (1), Flavasperone (2), Aurasperone A (3), Asperpyrones C (4), Asperpyrones B (5) and Fonsecinone A (6) were isolated from A. niger. In bioassays, compounds 1 through 6 showed different levels of antibacterial activities against pathogen bacteria. Flavasperone (2) and Asperpyrones C (4) showed potent antibacterial activities against S. aureus ATCC33591 with MIC values 43.7 and 21.9 μmol/L, respectively. Aurasperone A (3) exhibited significant activities against E. faecium ATCC35667 with MIC values 21.9 μmol/L. Compounds 1 through 6 displayed toxicity on brine shrimps larvae, the LD50 values of Flavasperone (2) and Aurasperone A (3) were 35.0 and 8.8 μmol/L, respectively. [Conclusion] Diverse naphthopyrones were produced by strain XJJ-3. Compounds 1 through 6 showed different levels of activities against pathogen bacteria and Artemia salina. This study may provide reference for the development of antibacterial and cytotoxic drugs.