The opaque ultrasound transducers used in conventional photoacoustic imaging systems necessitate oblique light delivery, which gives rise to some disadvantages such as inefficient target illumination and bulky system size. This work proposes a transparent capacitive micromachined ultrasound transducer (CMUT) linear array with dual-band operation for through-illumination photoacoustic imaging. Fabricated using an adhesive wafer bonding method, the array consists of optically transparent conductors [indium tin oxide (ITO)] as both top and bottom electrodes, a transparent polymer [bisbenzocyclobutene (BCB)] as the sidewall and adhesive material, and largely transparent silicon nitride as the membrane. The fabricated device had a maximum optical transparency of 76.8% in the visible range. Furthermore, to simultaneously maintain higher spatial resolution and deeper imaging depth, this dual-frequency array consists of low- and high-frequency channels with 4.2- and 9.3-MHz center frequencies, respectively, which are configured in an interlaced architecture to minimize the grating lobes in the receive point spread function (PSF). With a wider bandwidth compared to the single-frequency case, the fabricated transparent dual-frequency CMUT array was used in through-illumination photoacoustic imaging of wire targets demonstrating an improved spatial resolution and imaging depth.