Display omitted •Three new highly oxygenated azaphilones were isolated from Penicillium sp. LZUC-S1.•Compound 1 belongs to a rare class of azaphilone possessing an acetonyl at C-8.•Some azaphilones showed antifungal activity against four phytopathogenic fungi. Three new highly oxygenated azaphilones, penicilphilones A–C (1–3), along with four known analogues (4–7) were isolated from the culture of Penicillium sp. LZUC-S1. Their structures were elucidated by detailed spectroscopic data interpretation, electronic circular dichroism (ECD) calculation, and DP4+ analysis. 1 belongs to a rare class of azaphilone possessing an acetonyl at C-8. 2, 5, and 6 are uncommon azaphilones holding a chain with four carbons at C-8. Compounds 1, 3, and 4 showed potent activities against the selected phytopathogenic fungi with inhibitory rates ranging from 49.8 to 78.6 % at 50 μg/mL. In addition, a putative biogenetic pathway for compounds 1, 2, 5, and 6 was proposed.