Photoacoustic molecular imaging, by combing the photoacoustic tomography and molecular imaging, is a novel biomedical imaging modality that can image tissue non-invasively and in vivo. This modality has high imaging depth, resolution, and specificity. Photoacoustic molecular imaging has been widely used in animal experiments, achieving many promising results. We describe the fundamental mechanism of this modality, review its current research activities, and discuss its prospects.