The implementation of hybrid fluorescence molecular tomography (FMT) and X-ray computed tomography (CT) has been shown to be a necessary development, not only for combining anatomical with functional and molecular contrast, but also for generating optical images of high fidelity and quantification accuracy. FMT affords highly sensitive three-dimensional imaging of fluorescence bio-distribution throughout animal bodies but in stand-alone form it offers images of low resolution. It was shown that FMT accuracy significantly improves by considering anatomical priors from X-ray computed tomography (CT). Conversely, X-ray CT generally suffers from low soft tissue contrast. Therefore utilization of X-ray CT data as prior information to the fluorescence inversion problem is challenging in applications where different internal organs are not clearly differentiated. Instead, we combined herein FMT with emerging X-ray phase-contrast computed tomography (PCCT). PCCT relies on the phase shift differences in tissue to deliver anatomical images of biological samples with superior soft tissue contrast than conventional absorption-based CT. We demonstrate for the first time hybrid FMT-PCCT imaging of different animal models, where FMT and PCCT scans were performed in vivo and ex vivo, respectively. The results show that FMT-PCCT expands the potential and utility of FMT in imaging lesions which show otherwise low or no contrast in conventional CT, while retaining the cost benefits and technical simplicity of CT and single hybrid devices. The results point to the most accurate hybrid FMT performance to date.