This research investigated bioactive compounds produced by endophytic fungi isolated from healthy young and mature leaves, branches and barks of Croton oblongifolius from sites on Chulalongkorn University. Endophytic fungi 47 isolates were isolated from plant samples by surface sterilization method and placed on malt extract agar. Endophytic fungal isolate CuLm17 was chosen for study of bioactive compounds because this isolate produced the compounds that were active against a large number of test microorganisms with highest activities. Based on morphology endophytic fungal isolate CuLm17 was identified as Penicillium sp. Ethyl acetate (EtOAc) crude mycelial extract of Penicillium sp. was separated by chromatographic techniques and was purified by crystallization. Isolation and purification of EtOAc crude mycelial extract gave two pure compounds. The structure elucidation of these compounds was achieved by a combination of spectroscopic methods (IR, MS, UV, [superscript 1]H, [superscript 13]C NMR and 2D NMR), physical properties and the structure of compound ME1 was confirmed by X-ray analysis. It found that compound ME1 was folipastatin and compound ME2 was unguinol. Moreover, folipastatin was inhibitory against B. subtilis ATCC 6633, S. aureus ATCC 25923, E. coli ATCC 25922 and P. aeruginosa ATCC 27853 with MIC value of 164.5, 657.9, 328.9 and 328.9 micrometre, respectively and displayed high cytotoxic activity against HEP-G2 (hepatoma), SW 620 (colon), CHAGO (lung), KATO-3 (gastric) and BT474 (breast) with IC[subscript 50] value of 15.7, 15.3, 14.5, 15.8 and 22.6 micrometre, respectively. Unguinol was inhibitory against B. subtilis ATCC 6633, S. aureus ATCC 25923, E. coli ATCC 25922 and P. aeruginosa ATCC 27853 with MIC value of 191.7, 1533.7, 1533.7 and 1533.7 micrometre, respectively and displayed cytotoxic activity against KATO-3 (gastric) with IC[subscript 50] value of 21.2 micrometre. On the other hand, folipastatin and unguinol were not shown antioxidant activity. This research was the first report for isolation and studying bioactive activities of folipastatin and unguinol from Penicillium sp. endophyte.