There are MANY cities in Japan. It's a country, just like the US, Russia,or Mexico! However, the most recognized cities by the average commoner would be Tokyo; and, of course Hiroshima and Nagasaki, made famous by the World War II nuclear weapon phenomenon.
Another popular city is Kyoto, made ever so famous by the the movie "The Last Samurai," starring Tom Cruise.
Other Japanese cities: They are alphabetized:
Aichi, Akita, Aomori, Chiba, Ehime, Fukui, Fukuoka, Fukushima, Gifu, Gunma, Hiroshima, Hokkaidō, Hyōgo, Ibaraki, Ishikawa, Iwate, Kagawa, Kagoshima, Kanagawa, Kōchi, Kumamoto, Mie, Miyagi, Miyazaki, Nayoga, Nagasaki, Nara, Niigata, Ōita, Okayama, Okinawa, Osaka, Saga, Saitama, Shiga, Shimane, Shizuoka, Tochigi, Tokushima, Tokyo, Tottori, Toyama, Wakayama, Yamagata, Yamaguchi, and Yamanashi.