We present the first hybrid photoacoustic fluorescence molecular tomography system, capable of three-dimensional imaging of both fluorochrome and chromophore distributions in highly scattering and absorbing tissue. Quantitative three-dimensional maps of optical absorption coefficient are acquired using photoacoustic tomography. The reconstructed absorption data is fed into the Fluorescence Molecular Tomography inversion scheme in order to improve its accuracy and quatification capabilities in the presence of strong and distributed absorbers that are expected to bias stand-alone fluorescence reconstructions. At all, having both techniques in one hybrid modality yields a system that combines high molecular specificity and targeting flexibility of fluorescent imaging and high spatial resolution functional information obtained via photo-acoustic images.