Five new prenylxanthones, ruguloxanthones A-C (1-3), 14-methoxytajixanthone (4), and tajixanthone ethanoate (5), a new bicyclo[3.3.1]nona-2,6-diene derivative, rugulosone (6), and seven known compounds, shamixanthone, tajixanthone, 14-methoxytajixanthone-25-acetate, tajixanthone hydrate, tajixanthone methanoate, isoemericellin, and ergosterol, were isolated from the fungus Emericella rugulosa. The structures of 1-6 were established using spectroscopic techniques. Compound 6 exhibited antimalarial and antimycobacterial activities, as well as cytotoxicity against three cancer cell lines.