There is increasing interest in studying molecular-based devices that perform Boolean logic operations whose output state (0 or 1) depends on the input conditions (0/0, 1/0, 0/1, or 1/1). So far, great efforts have been devoted to establish molecular-scaled logic gates activated by chemical, physical, and biological inputs. We herein describe the design and synthesis of a tandem protein kinase substrate peptide acting as a phosphate-mediated molecular memory. The molecular-based memory system is comprised of two different phosphorylatable substrate regions joined in series and a spiropyran derivative at the N-terminus. We also demonstrated three basic "AND", "OR", and "NOR" logic operations on the basis of alterations in the spiropyran-to-merocyanine (SP-to-MC) thermocoloration properties of the spiropyran moiety in the peptide upon kinase-catalyzed phosphorylation. The three logic functions were successfully performed by adding ionic polymers as programming elements with preset thresholds of a signal intensity in a microplate format. Throughout this study, information was recorded on the substrate peptide by protein kinase-catalyzed phosphorylation, stored stably as phosphoesters, read according to the extent of the SP-to-MC thermocoloration, and erased by phosphatase-catalyzed dephosphorylation, resulting in the peptide returning to the initial recordable state. Thus, the proof-of-concept experiments described herein could be used to provide clues for developing practical molecular-based processing and computing.