High intensity focused ultrasound (HIFU) treatment is a promising non-invasive method for killing or destroying the diseased tissues by locally delivering thermal and mechanical energy without damaging surrounding normal tissues. In HIFU, measuring the temperature at the treatment site is important for improving the therapeutic efficacy, controlling safety, and appropriately planning a treatment. A conventional method for measuring the temperature is using magnetic resonance imaging (MRI), which is limited by its slow frame rate, bulky and expensive hardware, and the compatibility issue with the HIFU machine. Several researchers have proposed photoacoustic thermometry for monitoring HIFU treatment, but they had many limitations, including not being able to acquire images while the HIFU is on, incapability of real-time image-based monitoring, or inappropriate configuration to be translated for clinical applications. In this paper, we propose a novel integrated real-time photoacoustic thermometry system for HIFU treatment monitoring. The system provides ultrasound B-mode imaging and photoacoustic structural imaging in real-time, which can be used for photoacoustic thermometry during HIFU treatment for both in vitro and in vivo environments without any interference from the strong therapeutic HIFU waves. By properly controlling the imaging and treatment sequences, we have successfully shown the real-time ultrasound and photoacoustic imaging without any interference from the simultaneous HIFU treatment. Based on this capability, we have demonstrated the photoacoustic thermometry by investigating the relationship between the photoacoustic amplitude and the measured temperature during HIFU treatment with in vitro phantoms and in vivo tumor-bearing mice. The results show the feasibility of a clinically potential real-time photoacoustic thermometry system for safe and effective monitoring of HIFU treatment.