Submerged tropical karst features were discovered in Nagura Bay on Ishigaki Island in the southern Ryukyu Islands, Japan. The coastal seafloor at depths shallower than similar to 130 m has been subjected to repeated and alternating subaerial erosion and sedimentation during periods of Quaternary sea-level lowstands. We conducted a broadband multibeam survey in the central area of Nagura Bay (1.85 x 2.7 km) and visualized the high-resolution bathymetric results over a depth range of 1.6-58.5 m. Various types of humid tropical karst landforms were found to coexist within the bay, including fluviokarst, doline karst, cockpit karst, polygonal karst, uvalas, and mega-dolines. Although these submerged karst landforms are covered by thick postglacial reef and reef sediments, their shapes and sizes are distinct from those associated with coral reef geomorphology. The submerged landscape of Nagura Bay likely formed during multiple glacial and interglacial periods. According to our bathymetric results and the aerial photographs of the coastal area, this submerged karst landscape appears to have developed throughout Nagura Bay (i.e., over an area of approximately 6 x 5 km) and represents the largest submerged karst in Japan.