Production of secondary metabolites by filamentous fungi, such as sclerotiorin from Penicillium sclerotiorum, sometimes is limited to solid state fermentation or submerged culture without stirring (mycelial mat on air-liquid surface). In the present work, sclerotiorin was isolated and identified by submerged culture of the marine-derived P. sclerotiorum FS50 in Czapek medium without stirring while no sclerotiorin observed by submerged culture with stirring under the same condition. It was found that low pH (below 6 via adjustment of nitrogen and phosphorus concentration in the Czapek medium) led to sclerotiorin accumulation by submerged culture with stirring (mycelia acting as planktonic cells). Replacement of NaNO3 in the Czapek medium with NH4Cl further confirmed that maintaining pH 4-6 was key to accumulation of sclerotiorin by submerged culture with stirring.