Consecutive spectral analyses of ultraweak photon emission from sweet potato showing a defense response were conducted to observe the process of physiological transition. The spectrum showed a drastic transition from 2 to 10 h after inoculation with Fusarium oxysporum, during which the emission intensity increased slowly. The spectrum was stable from 10 to 36 h after inoculation, whereas the emission intensity peaked approximately 20 h after inoculation. A change in the physiological state connected with the synthesis of defense-related substances is suggested as contributing to this phenomenon. The spectral transition was also detected in sweet potato treated with growth hormone or exposed to alternating temperature, although with an extremely weak emission intensity. This spectral analysis of ultraweak photon emission can be used as a new means for identifying the physiological state.