Abstract: With the emergence of in vivo optical imaging, bioluminescence imaging and fluorescence imaging can be used to non-invasively monitor the activities and responses of cells marked with optical signals in real time, which are considered to be promising tools for tumor detection, gene expression profiling, protein molecular detection, drug receptor localization, drug screening, and therapeutic evaluation. In this paper, the features, imaging systems, and applications of in vivo bioluminescence imaging and in vivo fluorescence imaging have been introduced and compared in detail. The basic theories, application fields, and development of in vivo optical imaging in future are reviewed.