Three new naphthoquinones, astropaquinones A-C (1-3), were isolated from cultures of the freshwater fungus Astrosphaeriella papuana YMF 1.01181, together with the known compound, 6-hydroxy-2,4-dimethoxy-7-methylanthraquinone (4). The structures of the compounds were settled mainly by interpretation of their 1D and 2D NMR spectra. Astropaquinone B (2) and C (3) were found to possess a rare pyranonaphthoquinone skeleton containing a lactol ring. Furthermore, compounds 1-4 showed moderate antagonistic activity against nine fungi and four bacterial strains.