Herbicidal activity-guided isolation from the fermentation extract of Penicillium viridicatum had obtained two herbicidal series of polyketides (1−7) and diketopiperazine derivatives (8−11), especially including three novel polyketides (1−3). The structures and absolute configurations of new polyketides 1−3 were elucidated by extensive spectroscopic analyses, as well as comparisons between measured and calculated ECD spectra. Novel polyketides 1−3 and known 4, all bearing the heptaketide skeleton with a trans-fused decalin ring of 8-CH 3 substitution, could significantly inhibit the radicle growth of Echinochloa crusgalli seedlings with a dose-dependent relationship. Especially at the concentration of 10 μg/mL, 1−4 exhibited the inhibition rates with 81.5% ± 2.0, 76.4% ± 0.8, 79.6% ± 1.1, and 80.0 ± 1.8%, respectively, even better than the commonly used synthetic herbicide of acetochlor with 76.1 ± 1.4%. Further greenhouse bioassay revealed that 4 showed pre-emergence herbicidal activity against E. crusgalli with the fresh-weight inhibition rate of 74.1% at a dosage of 400 g ai/ha, also better than acetochlor, while the other isolated metabolites (5−11) exhibited moderate herbicidal activities. The structure−activity differences of isolated polyketides indicated that the heptaketide skeleton, characterized by a trans-fused decalin ring with 8-CH 3 substitution, should be the key factor of their herbicidal activities, which could give new insights for the bioherbicide developments.