Bioluminescence tomography (BLT) is a new molecular imaging mode, which is being actively developed to reveal molecular and cellular signatures as labeled by bioluminescent probes in a living small animal. This technology can help diagnose diseases, evaluate therapies, and facilitate drug development with mouse models. In this paper, we describe in vivo mouse experiments with BLT, and propose the reconstruction procedure of bioluminescent sources from optical data measured on the body surface of the mouse using a modality fusion approach. The results show the feasibility of our methodology for localization and quantification of the bioluminescent activities in vivo.