Ultrasound imaging, one of the common diagnosis techniques, is frequently used since it is safe, cost-efficient technique and real-time imaging can be conducted. However, various organs and tissues reflect ultrasonic waves, which leads to difficulty in imaging small biomolecules and to a low spatial resolution for deep-tissue images. As such, there have been significant advances in photonics and optical molecular probes in recent years, and photoacoustic (PA) tomography (PAT) has emerged as a promising modality that can overcome the limitations of ultrasound. PAT relies on the photoacoustic effect, which is the conversion of absorbed optical energy into acoustic energy. Since fewer biomolecules exhibit the photoacoustic effect compared to the scattering or reflection of ultrasound, PAT can be employed to generate high-resolution images. PAT also has a number of other advantages when compared to conventional biomedical imaging modalities such as optical tomography, ultrasound imaging, computed tomography, positron emission tomography and magnetic resonance imaging. This review provides a general overview of the contrast agents used for PAT, including organic, inorganic and hybrid contrast agents, and describes their application. This review also identifies limitations of current PAT contrast agents and suggests future research directions for their development.