Nine diketopiperazines were characterized from the culture of marine fungal isolate MR2012 which based on DNA amplification and sequencing of the fungal internal transcribed spacer (ITS) region was identified as Aspergillus fumigatus. The isolated fungal metabolites 4–12 were unambiguously identified as a series of simple and re-arranged diketopiperazines by analysis of spectroscopic data. t-Butoxycarbonyl group (BOC) derivatization was used to separate the intractable mixture of 4 and 5. When all compounds were evaluated for antimicrobial activity against gram positive bacteria, the isolated metabolites showed moderate to weak effects, while the semisynthetic derivatives 4a and 5a displayed strong activity comparable to the positive control, tetracycline against gram positive bacteria.