[Objective] We identified fungus BYSTW3, from Odontotermes formosanus, and studied its active secondary metabolites. [Methods] BYSTW3 was identified by morphological observation and ITS (Internal Transcribed Spacer) sequence analysis. The antibacterial and antifungal activities of crude extracts were tested by filter paper method and growth rate method respectively. The crude extracts were separated and purified by a variety of chromatographic column separation methods, and the structures of the compounds were analyzed with a variety of spectral data. [Results] Strain BYSTW3 was identified as a potential new species of Pleosporales sp. The crude extract of BYSTW3 inhibited radical growth of Valsa mali and Fusarium oxysporum f. sp. mornordicae with the inhibition rates of 54.5% and 53.4% at the concentration of 100 μg/mL. Bioactivity-guided fractionation lead to the isolation of three fungal metabolites 1−3, including physcion (1), FK-17-p2a (2) and citrinin (3). Both compounds 1 and 3 were firstly isolated from the fungus of Pleosporales sp.. At the concentration of 30 μg/disc, compound 3 showed potent antibacterial activity against Staphyloccocus aureus, Bacillus subtilis and Escherichia coli with the mean halo diameter of 23.0 mm, 24.2 mm and 20.7 mm, respectively. [Conclusion] BYSTW3 is a potential new strain with good prospects as a new antimicrobial agents from microbial resources.