Two new chromone derivatives, 2-hydroxymethyl-3-methyl-7-methoxychromone (1) and 2-hydroxymethyl-3- tert-butyl-7-methoxychromone (2), together with a related known compound, 2,3-dimethyl-7-methoxychromone (3), were isolated from Rhinocladiella sp. (IO2), a fungus obtained from the sponge Ircinia oros. Furthermore, a new isocoumarin derivative, 3-(3-chloro-2-hydroxypropyl)-8-hydroxy-6-methoxy-isochromen-1-one (4) and a known analogue 3-[( R)-3,3-dichloro-2-hydroxypropyl]-8-hydroxy-6-methoxy-1 H-isochromen-1-one (dichlorodiaportin, 5), were identified from sponge-derived fungal strain Clonostachys sp. (AP4.1), while a new indole alkaloid 1-(4-hydroxybenzoyl)indole-3-carbaldehyde (6) was obtained from the sponge-derived fungus Engyodontium album (IVB1b). The structures of these compounds were established by NMR spectroscopic and mass spectrometric data analysis, as well as by comparison with literature reports. Compounds 4 and 6 were examined for cytotoxic and antimicrobial activities, respectively. None of them showed potent activity.