Marine bacteria are an interesting issue for searching of natural bioactive compounds when rising up of drug resistant bacteria and incurable diseases. This is the first report on pure bioactive compounds from a Bacillus sp. strain C-1-10 isolated from the soft coral Alcyonium digitatum in the Baltic Sea. The strain C-1-10 showed capable of yielding at least 7 natural compounds on both Glucose Yeast Malt medium and Bannett medium. The pure compounds were isolated with semi-preparative high-performance liquid chromatography (HPLC). Four purified natural substances are tested for antimicrobial activities, antifungal, cytotoxic and enzyme inhibition. All four compounds showed inhibition of Staphylococcus epidermidis and Staphylococcus aureus MRSA. The compound 5 showed rather weak inhibition of Gram-negative Escherichia coli and was inactive to phosphodiesterase 4, while the other compounds were inactive to E. coli and active against phosphodiesterase 4. However, all four pure compounds were inactive to other Gram-negative bacteria and fungi and exhibited no cytotoxic activity, and no inhibition to glycogen synthase kinase, and protein-tyrosine-phosphatase. A soft coral derived Bacillus sp. strain C-1-10 showed a promised strain for bioactive compound producing.