Bioassay-guided fractionation of the organic extracts of the endophyte Daldinia eschscholtzii strain GsE13 led to the isolation of several phytotoxic compounds, including two chromenone and two chromanone derivatives: 5-hydroxy-8-methoxy-2-methyl-4H-chromen-4-one, 1; 5-hydroxy-2-methyl-4H-chromen-4-one, 2; 5-methoxy-2-methyl-chroman-4-one, 3; and 5-methoxy-2-methyl-chroman-4-ol, 4; as well as other aromatic compounds: 4,8-dihydroxy-1-tetralone, 5; 1,8-dimethoxynaphthalene, 6; and 4,9-dihydroxy-1,2,11,12-tetrahydroperyl-ene-3,10-quinone, 7. Compounds 1, 4, and 7 were isolated for the first time from D. eschscholtzii. The phytotoxicity of all the compounds was determined on germination, root growth, and oxygen uptake in seedlings of a monocotyledonous (Panicum miliaceum) and three dicotyledonous plants (Medicago sativa, Trifolium pratense, and Amaranthus hypochondriacus). In general, root growth was the most affected process in all four weeds, and chromenones 1 and 2 were the most phytotoxic compounds. Phytotoxins 1-4 inhibited basal oxygen consumption rate in isolated mitochondria from M. sativa seedlings and also caused serious damage to their membrane potential (Delta psi m) in percentages greater than 50% at concentrations lower than 2 mM. Based on these results, compounds 1-4 of endophytic origin could be promising for the development of new herbicides potentially useful in agriculture or for the synthesis of promising new molecules.