Two new compounds, including a chlorinated indole-diterpenoid 19-hydroxypenitrem A (1) and its dechlorinated derivative 19-hydroxypenitrem E (2), along with two known congeners (3 and 4), were isolated and identified from the cultures of Aspergillus nidulans EN-330, an endophytic fungus obtained from the marine red alga Polysiphonia scopulorum var. villum. Their structures and absolute configurations were assigned on the basis of 1D and 2D NMR and CD experiments. Compounds 1–4 exhibited cytotoxic activity against brine shrimp with LD50 values of 3.2, 4.6, 1.7, and 8.7 mM, respectively. Besides, the chlorinated 19-hydroxypenitrem A (1) showed antimicrobial activity against four human- and aqua-pathogens. Preliminary SAR study revealed that the Cl-substitution at C-6 enhanced the cytotoxic activity against brine shrimp and antimicrobial activity, while the 19-OH substitution suppressed the activity.