The lancelet is an important animal in evolutionary studies. Artificial proliferation is necessary to secure individuals for experiments. However, the number of individuals and their habitats are decreasing remarkably in the Ariake Sea. Despite the transplantation of frys, the number of adults has not increased. In addition, basic data such as water parameters and bottom conditions in the habit have not been clarified. The geography, oceanography and geology of the largest habitat in the Ariake Sea were investigated using acoustic machines and an AUV. The cause of the decrease in individuals is presumed not to be a result of an increase of mud in the sediments, but due to lancelets being preyed upon by rays based on CCD camera and side scan sonar images taken by the AUV. These results show the utility of AUVs in important discoveries of the biology of the hydrosphere.