For efficient antibacterial photodynamic therapy for wounds, information on the distribution of a photosensitizer in tissue is important, but conventional fluorescence measurement does not provide depth-resolved information. We previously proposed in vivo photoacoustic (PA) depth profiling of a photosensitizer, but the contrast of PA signals was not sufficiently high, mainly due to light absorption by blood in tissue. In this study, we performed dual-wavelength PA measurement; green light and red light were used to excite blood and photosensitzer, respectively, and the former signal was subtracted from the latter signal to compensate a blood-associated component. Methylene blue or porfimer sodium solution was injected into subcutaneous tissue in rats with deep dermal burn and two-dimensional PA measurement was performed. The signal subtraction diminished not only the signal originating from blood but also the signal originating from the stratum corneum and acoustic reflection noise, creating a high-contrast PA image. The distribution of PA signals was confirmed to coincide well with the distribution of photosensitizer-originating fluorescence measured for tissue biopsied after the PA measurement, demonstrating the validity of this method for in vivo photosensitizer dosimetry. On the basis of this method, temporal behaviors of two photosensitizers were compared.