Metabolites isolated from Penicillium palitans, obtained from deep sea sediments in the maritime Antarctica, were investigated for phytotoxic and antifungal activities. The fungus was submitted to solid state fermentation, and its crude extract was produced. Chromatographic separations of the P. palitans methylene chloride crude extract led to the isolation of two analogous compounds: (−)‐penienone (1) and (−)‐palitantin (2). The phytotoxic activity of these compounds was assessed against seeds of Lactuca sativa and Agrostis stolonifera. Both compounds demonstrated activity exclusively in the monocotyledonous model, A. stolonifera. At a concentration of 1 mg mL−1, (−)‐penienone caused 100 % inhibition of seed germination, while (−)‐palitantin had only moderate activity on germination and growth of seedlings at this concentration after 7 days of treatment. Against Lemna paucicostata, at 57 μM, (−)‐penienone inhibited growth by 50 % (IC50). (−)‐Palitantin was much less active. When evaluated for their antifungal activity against Colletotrichum fragariae, only (−)‐penienone had an IC50 value of 0.3 μM. The strain P. palitans was shown to be a promising source of phytotoxic and antifungal compounds, suggesting that extremophilic fungi, such as wild Penicillium strains from Antarctica, have the potential to yield novel prototype molecules for new pesticide development.