[Objective] We isolated and identified the natural products with antibacterial activity from fungal strain WH4-2.[Methods] We identified strain WH4-2 by colonial morphological traits and ITS sequence analysis, used activity-oriented method to isolate secondary metabolites, elucidated structures by spectrographic analysis, adopted micro-dilution method to assay antibacterial activity. [Results] We identified strain WH4-2 as Talaromyces stipitatus. Activity-oriented separation resulted in the isolation of compound 1 (5S-arugosin K), 2 (5R-arugosin K), 3 (5S-arugosin M), 4 (5R-arugosin M) and 5 (Chrysophanol), Compounds 1 through 4 were elucidated as isopentenyl dibenzo[b,e] oxepinone, compound 5 was anthraquinone. Compounds 1 through 4 showed potent antibacterial activities against S. aureus ATCC43300, ATCC33591, E. faecium ATCC35667 and B. subtilis ATCC6633.[Conclusion] The antibacterial compounds isolated from fungus T. stipitatus were isopentenyl dibenzo[b,e] oxepinone enantiomers.