The Seto Inland Sea is the largest enclosed coastal sea in Japan and is also a major fishing ground including aquacultures of fish, bivalves and seaweeds. The incidents of red tides dramatically increased in frequency and scale in the Seto Inland Sea along with serious eutrophication in the 1960s and 1970s. The maximum incident of 299 was recorded in 1976, but the incident has since shown a clear decreasing trend, reaching about 100 per year in the late 1980s by virtue of regulation by law, and this level has been maintained thereafter with the level of nutrients supporting red tide occurrences. The “Law Concerning Special Measures for Conservation of the Environment of the Seto Inland Sea” was legislated in 1973 and industrial loading was decreased to half the level of 1972. The important red tide organisms causing huge fishery damages by fish-kill are Chattonella antiqua, C. marina, C. ovata and Heterosigma akashiwo (Raphidophyceae), and Karenia mikimotoi and Cochlodinium polykrikoides (Dinophyceae). The maximum fishery damage (death of 14.2 million yellowtails) was 7.1 billion yen (about US $60 million) caused by C. antiqua in Harima-Nada in 1972. In 1988, a novel red-tide dinoflagellate species Heterocapsa circularisquama appeared for the first time, and has repeatedly killed both natural and aquacultured bivalves, with the highest damage of 3.9 billion yen to cultured oysters in Hiroshima Bay in 1998. Among the important red-tide organisms, C. antiqua, H. circularisquama and C. polykrikoides are rated as extremely harmful species that can easily reach the warning level of fishery damage by consuming only small amounts of nutrients. In toxic blooms, the dinoflagellate Alexandrium tamarense has become dominant in the Seto Inland Sea in the spring season, causing toxicity in short-necked clams and cultured oysters almost every year. Many countermeasures have been applied for harmful algal blooms in Japan. Laws for the regulation of water quality have been most effective in decreasing red-tide occurrences. No physical and chemical controls have been successful except for clay treatments. Clay spraying has been investigated and implemented in Kyushu and Korea for the removal of C. polykrikoides red tides. As environment-friendly mitigation strategies for red tides, biological controls using algicidal bacteria and viruses are proposed. A new finding of the abundant existence of algicidal bacteria on the surface of seaweeds suggests that co-culturing fish and seaweed is a prevention strategy for harmful algal blooms by virtue of the continuous release of many algicidal bacteria to the surrounding seawater. The artificial development of seaweed beds would also be effective as a prevention strategy for red tides.