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The thermophilic fungus Penicillium species was isolated from Ghamiqa hot spring sediments in Saudi Arabia. Extract of Penicillium species cultured on solid rice medium yielded two new compounds 3-(furan 12-carboxylic acid)-6-(methoxycarbonyl)-4-hydroxy-4-methyl-4 and 5-dihydro-2H-pyran 1 3α-methyl-7-hydroxy-5-carboxylic acid methyl ester-1-indanone 2. In addition, three known compounds, austinol 3, emodin 4, and 2-methyl-penicinoline 5, were isolated. The structures of the new compounds were unambiguously determined by comprehensive analysis of spectroscopic data, one- and two-dimensional NMR spectroscopy, and high-resolution mass spectrometry. All isolated metabolites were studied for their antibiotic effect against several pathogenic bacteria and for their cytotoxicity against the lymphoma human cancer cell line HTB-176. Austinol 3 exhibited strong antibacterial activity against P. aeruginosa bacterial strain with an MIC value of 0.13 ± 0.4 µg·mL−1, whereas emodin 4 demonstrated significant cytotoxicity against the tested HTB-176 cell line with an IC50 value of 2 ± 7.6 µM, while the other compounds were moderate to inactive with IC50 ranging from 4.3 ± 0.25–22 ± 2.94 µM in this assay.