Three sea turtle species (loggerhead [Caretta caretta], green [Chelonia mydas], and hawksbill [Eretmochelys imbricata] turtles) have nesting sites at Ishigakijima Island, which is located in the southwestern part of Japan. This island is known as the geographic southern (low-latitude) limit of north Pacific loggerhead turtles' nesting sites and close to the northern (high-latitude) limit of northwest Pacific green and hawksbill turtles' nesting sites. Our 26-yr nesting survey (1993–2018) revealed that the number of nesting events of loggerhead turtles decreased (with a temporal increment between 2006 and 2008), while the other study reported that the entire Japanese loggerhead nesting population continued to increase substantially from 2006 to, at least, 2012. In contrast, the green turtle population increased gradually, with fluctuations. Hawksbill turtles had several nests annually. The sea surface temperature during the nesting season was significantly related to the annual number of nesting events in loggerhead turtles but not in green and hawksbill turtles. Thus, warming temperature may have caused a reduction in the nesting population of loggerhead turtles at Ishigakijima Island, which is the southern limit of their nesting distribution.