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Continuous long-term monitoring is important for detecting ecological changes and understanding their causes, including anthropogenic impacts such as climate changes and eutrophication. Nonetheless, such long-term population studies have been rare, especially for sea urchins, which can affect community dynamics owing to their extensive herbivory and large population fluctuations. Here we present a long-term (from 1963 to 2014) dynamics of sea urchins in a fixed quadrat on a lower intertidal rocky flat in Hatakejima Island, southern Japan. We also conducted a complementary survey over the entire island approximately every five years from 1975 to 2013, and a 41-year assay for developmental abnormality of the sea urchin Heliocidaris crassispina using water adjacent to the island. The abundance of three commonest species in this area (H. crassispina, Echinostrephus malaria, and Echinometra spp.) and the richness of urchin species showed large variations, with high numbers in the 1960s and 1970s, followed by an abrupt decline in the late 1970s or early 1980s, and a gradual recovery subsequently. The species abundance and richness in the entire island survey showed good correlations with those in the quadrat census. Statistical analyses indicated that increasing water temperature and red tides were the major factors influencing the dynamics of abundance and species richness. Our studies reveal that anthropogenic environmental changes influence the long-term dynamics in abundance and richness of sea urchins.