Several volcanic islands and submarine volcanoes exist in the sea connecting the Izu-Bonin Islands with the Mariana Islands, with trenches and islands formed by the submergence of the Pacific Plate under the Philippine Sea Plate. Although designated as a Marine Protected Area (MPA) in December 2020, the seamounts’ biodiversity has not been sufficiently researched. Therefore, direct observations and specimen sampling were conducted on four seamounts in this area using a remotely operated vehicle (ROV), autonomous underwater vehicle (AUV), and baited cameras (BCs). The ROV survey was conducted for 2–4 days on each seamount and divided into shallow and deep areas. During the expedition, 20 orders and 51 families of 81 deep-sea fish species were observed, including several potentially undescribed species, new genus or species records from Japanese waters, new depth records, new ecological information, and several rare fishes. The fish fauna and biodiversity abundance clearly differed among the seamounts; the seamount with a hydrothermal vent had the lowest diversity among the four seamounts. In shallow water, 23, 7, and 12 species were recorded only by ROV, AUV, and BC, respectively, indicating that combining these methods is beneficial for understanding the fish fauna of seamounts.