An organic solvent for extracting prodigiosin from culture broth was selected and a test to determine the long-term stability of prodigiosin was performed to develop prodigiosin as a biological control agent against Chattonella antiqua, a harmful alga that can cause red tides. Prodigiosin was extracted using nine solvents, and the extracts were analyzed by liquid chromatography-mass spectroscopy. Acetone was selected as the best organic solvent because of its high extraction efficiency and less processing time. Stability tests for prodigiosin were performed at various temperatures, and algicidal activity against C. antiqua was also tested. Ultimately, > 98% stability was sustained after 30 days at $4^{circ}C$, whereas < 30% stability was maintained after 30 days at $37^{circ}C$. Although prodigiosin was kept for 30 days in an optimum organic solvent, its stability was safely maintained and algicidal activity was sustained at $4^{circ}C$. These results indicate that acetone is a very useful extraction and storage solvent for prodigiosin.