Fungi isolated from mangrove rhizosphere soil of the South China Sea were investigated for the production of potential antifungal metabolites. With 28 fungal isolates, the strains Penicillium javanicum HK1-23 and P. janthinellum HK1-6 showed significant antifungal activities. A bioassay-guided investigation of the two fungal strains led to the isolation of two secondary metabolites, brefeldin A and penicillic acid, with high yields of 143 and 423 mg L −1, respectively. Penicillic acid showed potent antifungal activities toward Rhizoctonia solani and R. cerealis, with 67.5% and 76% growth inhibition, respectively, at 50 μg mL −1. Brefeldin A showed strong activity toward R. cerealis, with 56.4% growth inhibition at 50 μg mL −1. The research highlights the importance of exploring microbes from mangrove rhizosphere soil for the identification of bioactive metabolites for future fungicide development.