• Honshu. Honshu is the largest island of Japan and it is where the majority of the country's cities are located (maps). The Tokyo Osaka-Kyoto area is the core Honshu and Japan and 25% of the island's population lives in the Tokyo region. Kyushu. Kyushu is the third largest island of Japan and it is located to the south of Honshu (map). It has a total area of 13,761 square miles (35,640 sq km) and a 2006 population of 13,231,995 people. The largest city on Kyushu is Fukuoka and it is divided into seven prefectures.