Six isoindolone containing meroterpenoids, emericellolides A-C (1-3) and emeriphenolicins E-G (4-6), were isolated from a plant endophytic fungus Emericella nidulans HDN12-249. Emericellolides A-C (1-3) feature the unprecedented macrolide skeleton composed of an unusual l-glutamate fragment, an isoindolone unit, and a sesquiterpene moiety, while structures of emeriphenolicins E-G (4-6) with two farnesyl groups attached to one isoindolone unit are rare in isoindolone-derived meroterpenoids. These structures including the absolute configurations were established on the basis of MS, NMR, Mo2(AcO)4-induced ECD, Marfey's method, and chemical conversion. Compound 4 exhibited cytotoxicity against HeLa cells with IC50 value of 4.77 μM.