Sponge-associated fungi represent the single most prolific source of novel natural products from marine fungi. Cyclo (L-Trp-L-Phe) exhibits biological functions such as plant growth regulation, moderate cytotoxicity and thus has the application potential in pharmaceutical and agricultural biotechnologies. In this study, a fungal strain TS08 was isolated from sponge Holoxea sp. in the South China Sea and identified as A. versicolor according to its 18S rRNA gene and morphological, physiological, and biochemical characteristics. Meanwhile, cyclo (L-Trp-L-Phe) was found to be produced by A. versicolor strain TS08 mainly in the exponential growth phase. The highest yield of cyclo (L-Trp-L-Phe), 13.24 mg/g (per crude extract of EtOAc), 2.51% of cell dry weigh, was obtained on the tenth day of the fungal cultivation. It was the first time to find the biological active cyclo (L-Trp-L-Phe) in sponge-associated microorganism.