Chemical investigation of the mycelium of Edenia gomezpompae, a newly discovered endophytic fungus isolated from the leaves of Callicarpa acuminata (Verbenaceae) collected from the ecological reserve El Eden, Quintana Roo, Mexico, resulted in the isolation of four naphthoquinone spiroketals, including three new compounds and palmarumycin CP 2 ( 4). We elucidated the structures of the metabolites by extensive NMR spectroscopy studies, including DEPT, COSY, NOESY, HSQC, HMBC, and chiroptical methods. The trivial names proposed for these compounds are preussomerin EG 1 ( 1), preussomerin EG 2 ( 2) and preussomerin EG 3 ( 3). In addition, the X-ray data for 4 were obtained. The bioactivity of the mycelial organic extracts and the pure compounds was tested against three endophytic fungi ( Colletotrichum sp., Phomopsis sp., and Guignardia manguifera) isolated from the same plant species ( C. acuminata, Verbenaceae) and against four economically important phytopathogenic microorganisms (two fungoid oomycetes, Phythophtora capsici and Phythophtora parasitica, and the fungi Fusarium oxysporum and Alternaria solani). Spiroketals 1–3 displayed significant growth inhibition against all the phytopathogens. IC 50 values for the four phytopathogens were from 20 to 170 μg/ml. Palmarumycin CP 2 ( 4) was not bioactive against any of the fungi tested. Compound 1 showed the strongest bioactivity. The acetylated derivatives of preussomerin EG 1 ( 1), 1a and 1b, were obtained and their biological activity was tested on endophytes and phytopathogens. Preussomerin EG 1 1, 1a and 1b exhibited significant bioactivity against all microorganisms tested with the exception of Alternaria solani. This is the first report of allelochemicals with antifungal activity from the newly discovered endophytic fungus E. gomezpompae.