Photodynamic therapy (PDT) is an important treatment modality for cancer and other localized diseases. In addition to PDT dose, singlet oxygen (1O2) concentration is used as an explicit PDT dosimetry quantity, because 1O2 is the major cytotoxic agent in photodynamic therapy, and the reaction between 1O2 and tumor tissues/cells determines the treatment efficacy. 1O2 concentration can be obtained by the PDT model, which includes diffusion equation for the light transport in tissue and macroscopic kinetic equations for the generation of the singlet oxygen. This model was implemented using finite-element method (FEM) by COMSOL. In the kinetic equations, 5 photo-physiological parameters were determined explicitly to predict the generation of 1O2. The singlet oxygen concentration profile was calculated iteratively by comparing the model with the measurements based on mice experiments, to obtain the apparent reacted 1O2 concentration as an explicit PDT dosimetry quantity. Two photo sensitizers including Photofrin and BPD Verteporfin, were tested using this model to determine their photo-physiological parameters and the reacted 1O2 concentrations.