Photoacoustic tomography (PAT) as a hybrid technology combines the high optical contrast and high acoustic resolution in a single imaging modality. However, most of the available PAT systems cannot comprehensively or accurately characterize biological systems at multiple length scales due to the use of narrow bandwidth commercial ultrasonic transducers. In this study, we fabricated a novel multi-band capacitive micromachined ultrasonic transducer (CMUT) array, and first developed a CMUT-based multi-band photoacoustic tomography (MBPAT) imaging system. The MBPAT imaging system was examined by the phantom experiment, and then was successfully applied to image the zebrafish in vivo. The imaging results indicated that CMUT-array-based MBPAT can provide a more comprehensive and accurate characterization of biological tissues, which exhibit the potential of MBPAT/CMUT in various areas of biomedical imaging.