Marine symbiotic fungi represent an intriguing source of discovery of novel secondary metabolites with various biological activities. Sea anemones are benthic marine invertebrates, however, the cultivable symbiotic fungi residing in the sea anemones are paid few attentions compared to those derived from their cnidarian counterparts. Here we show the identification of antimicrobial secondary metabolites from the sea anemone-derived symbiotic fungi. Out of five isolated fungal strains, only the strain SMA01 showed strong antimicrobial activities, which was assigned into the genus Emericella based on the morphological characteristics and the ITS sequencing. Media swift from liquid fermentation to solid rice medium presented little influence on its antibacterial activity. A chemical investigation of the ethyl acetate extract of the Emericella sp. SMA01 led to discovery of the primary antibiotic metabolite phenazine-1-carboxylic acid. The IC50 values of the phenazine-1-carboxylic acid against Phytophthora capsici, Gibberella zeae, and Verticillium dahliae were determined to be 23.26–53.89 μg/mL. To the best of our knowledge, this was the first report of Emericella sp. in sea anemones. The current study may benefit understanding of the defensive chemical interactions between the symbiotic fungi and their host sea anemones.