Red Data Book is a book describing information on endangered wildlife, including species names, ecology, distribution, current status, and factors of population decline. In 2023, Toba City published a Red Data Book listing 429 endangered marine species inhabiting the coastal and estuarine areas around Toba City. The book describes the endangered categories of the listed species according to the degree of threat of extinction and the causes of population decline. In addition to the scientific information, the book includes many pictures of underwater surveys and seascapes, history and culture between local people and the sea, and sea-related folklore in the Toba area as column articles of the book. Unique feature of the Toba Red Data Book is that it specializes in marine organisms including algae or off-shore specie, and evaluate the vulnerability of marine species at the prefectural level. This dataset contains background data collected to evaluate vulnerability of the species in the Toba Red Data Book, and the data were quality controlled and transformed to comply with the Darwin Core, OBIS Schema.