To date, prodigiosin and its analogues which have been shown to have anticancer, cytotoxic and immunosuppressive activities have been isolated from Serratia, Pseudomonas and Streptomyces species, and chemically synthesized. In a previous study, the red pigment content in Serratia sp. KH-95 was enhanced using a casein-enriched medium. Recently, an integrated bioreactor with an internal adsorbent has been developed to increase the production yield and allow easy recovery of the pigment. Thus, this study focused on both purifying and identifying a single red pigment from several pigments attached to the adsorbent in an integrated bioreactor. The red pigment was extracted directly from the internal adsorbent using acidified methanol and phase separation. Subsequently, it was purified by silica gel chromatography and high performance liquid chromatograph (HPLC). As a result, pure prodigiosin was identified by structural studies as a pigment. Also, this downstream procedure that uses the integrated bioreactor can be applied to the direct production and purification of other prodigiosin analogues and hydrophobic alkaloid compounds from several microorganisms.