One of the major steps toward the industrialization of microbial product(s) is to optimize the cultivation conditions at the large scale bioreactor and successfully control the microbial behavior within large scale production environment. Statistical Design of Experiment was proven to optimize a vast number of microbial processes to achieve robustness and explore possible interactions among the variables. In this research, Taguchi Orthogonal Array was applied to optimize the cultivation condition of a newly isolated Prodigiosin-producing marine bacterial strain, Serratia AM8887, at bioreactor level. Two steps fermentation process was applied; as the productivity was scaled up from shake flask level to a bench top bioreactor (5L) and subsequently to an in-situ sterilization bioreactor system (20L) leading to a yield of 7g/L compared to 100mg/L prior to optimization confirming that; applying Taguchi experimental design is a reliable and good positive option for the optimization of biotechnological processes.. The produced pigment was purified and the chemical structure was revealed by means of Spectrophotometric, Maas Spectrum (MS), Fourier transform infrared (FT-IR), and proton nuclear magnetic resonance (1H-NMR) spectroscopy analysis. The biological activity including antibacterial, antioxidants and cytotoxicity to cancer cells line of the pigment were explored. The pigment showed very characteristic features that could helpful in food, pharmaceuticals and/or textile industries.