The Japan Oil, Gas and Metals National Corporation (JOGMEC) conducted the Kisoshisui (Tokaioki-Kumanonada) drilling campaign in the Nankai Trough area during 2003–2004 as part of the activities of the MH21 Research Consortium, which is supported by the Ministry of Economy, Trade and Industry (METI). Through this campaign, various subsea hydrate studies were conducted using various data, including logging while drilling, wireline, coring, and temperature measurement. Using recent technology, a precise in-situ temperature measurement system was successfully developed and deployed at the beginning of the drilling campaign. The goals of the study were to determine whether the measurement system and setup can reliably measure the equilibrium in-situ formation temperature, to determine if the measurements adequately delineate the geothermal gradient, and to identify any disturbances in the thermal regime of the hydrate-bearing sediment and the possible causes of the disturbances. The temperature of the hydrate-bearing sediment was monitored in a deep-water well for 1.5 months. Because the measurements were collected over a long period of time, the equilibrated formation temperatures could be readily determined after observing the thermal relaxation from drilling and sensor deployment effects. The temperature profile and the temperature gradient through the hydrate-bearing zone were estimated in a quasi–steady-state condition. A correlation between the tidal cycle and sea-floor temperature change is also discussed.