Hydrothermal activities are observed in Wakamiko Crater in Aira Caldera, south Kyushu, Japan. Wakamiko Crater is an active volcano that was formed by a big explosive eruption of Aira Caldera ca. 25 ka. Although Wakamiko Crater is characterized by many submarine active hydrothermal activities, its subsurface geothermal structures have not been clarified. Generally, it is difficult to obtain reliable heat flow values in shallow sea areas where the bottom water temperature is not stable and sedimentation rate is high. Hence, annual bottom sea water temperature variations were measured in order to correct the observed heat flow and the effect of the sedimentation rate.We observed under ground temperature at 95 points and determined marine surface heat flows at 44 points on between 2005 and 2009 in and around Wakamiko Crater. Hydrothermal site with hydrothermally alteredwhite patch or chimneys were found at 4 points in the crater. These results present that extremely high heat flow values (several hundred to 104 mW/m2) were observed near submarine hydrothermal sites, and these high values gradually decrease from the center of the Wakamiko Crater to the surrounding area. Heat flow values ranging 80to 100 mW/m2 around Wakamiko Crater represent the background heat flow values in south Kyushu. We also detected 51 nonlinear temperature profiles around Wakamiko Crater, which suggest water migration around the crater.