We examined the habitat use of the Indo-Pacific bottlenose dolphin Tursiops aduncus around Amakusa-Shimoshima Island, Japan. Of the approximately 200 individuals that resided in the waters north of this island, about 30 individuals moved to the south around Nagashima Strait, with different environments, and then disappeared. The habitat use of these dolphins in the south was examined using land- and boat-based surveys and compared with that in the north. The ferry crew sightings were also analyzed. Intensively used areas, which were estimated using a first-passage time analysis, were shallow waters close to the shore, located around small islands or in coastal areas facing the strait. Resting behavior, characterized by low apparent moving speed and synchronous dives, was observed in the intensively used areas. The dolphins tended to be on the south side of the strait in daytime hours, and the similar trend was observed at low and ebb tides. The habitat use, such as having certain resting places, possible habitat areas at night, and tidal-affected distribution was similar to that in the north. Resting places were scattered and not stable throughout the study period. The disappearance of dolphins may be due to drop in suitability of resting places.