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Dynamic fluorescence diffuse optical tomography (D-FDOT) is important for drug deliver research, as it allows to image the distribution of fluorescent biomarkers over time in vivo. In this letter, we visualize mouse liver perfusion after intravenous injection of indocyanine green (ICG) using a hybrid free-space FDOT and microcomputed tomography (micro-CT) system. In vivo dynamic tomographic images (110 frames; approximately 120 min) of mouse liver are reconstructed using structural a priori information provided by micro-CT, incorporating heterogeneous forward model. Further, the pharmacokinetic parameters of ICG in the liver, reflecting the uptake and excretion rate constants, are obtained using a two-compartmental model. The results show that we cannot only tomographically image the perfusion of fluorescent biomarkers in small animals on minute time scale (approximately 1.1 min/frame) but also obtain the corresponding pharmacokinetic parameters in vivo using the hybrid FDOT/micro-CT imaging system.