Marine natural products with biological activity represent an important resource for marine drugs and biotechnological products; however, most marine natural products, especially those derived from sponges, have not been further developed because of the limited number of sources. The scale-up cultivation of the microbial source of sponge-derived natural products could provide a possible approach to solve this bottleneck problem. In this study, statistical Plackett-Burman (PB) design and Box-Behnken response surface methodology (RSM) were used to optimize the medium components to increase the production of bacillamide C by the Bacillus atrophaeus strain C89, which was associated with the marine sponge Dysidea avara. The obtained optimal medium consisted of 3.64 g/L corn starch, 6.29 g/L CaCO3, 4.00 g/L soy peptone, 6.00 g/L peptone. 0.10 g/L cysteine and 0.02 g/L tryptophan with artificial sea water (ASW). Using this optimized medium, the concentration of bacillamide C reached 70.85 mg/L in fed-batch cultivation in a 5-L fermentor at pH 7.70, which was 25.80-fold higher than the level observed in a shake flask using the basic medium. This study provides a potential approach for the production of bacillamide C and related derivatives, which was the first to optimize the cultivation of sponge-associated microbes for the production of marine natural products. (C) 2011 Elsevier Ltd. All rights reserved.