1) Tokyo
Tokyo is Japan's capital and the country's largest city. It is one of Japan's 47 prefectures. The metropolis of Tokyo consists of 23 city wards, 26 cities, 5 towns and 8 villages, including the Izu and Ogasawara Islands, several small Pacific Islands in the south of Japan's main island Honshu.
The 23 city wards are the center of Tokyo and make up about one third of the metropolis' area, while housing roughly eight million of Tokyo's twelve million residents.
2) Kyoto
Kyoto was Japan's capital and the emperor's residence from 794 until 1868. It is now the country's seventh largest city with a population of 1.4 million people.
Over the centuries, Kyoto was destroyed by wars and fires, but due to its historic value, the city was not chosen as a target of air raids during World War II. Countless temples, shrines and other historically priceless structures still survive in the city.
3) Kamakura
Kamakura is a coastal town in Kanagawa, less than one hour south of Tokyo. Kamakura became the political center of Japan, when Minamoto Yoritomo chose the city as the seat of his new military government in 1192. The Kamakura government continued to rule Japan for over a century.
After the decline of the Kamakura government in the 14th century and the establishment of its successor, the Muromachi or Ashikaga government in Kyoto, Kamakura remained the political center of Eastern Japan for some time before losing its position to other cities.
Today, Kamakura is a very popular tourist destination. Sometimes called the Kyoto of Eastern Japan, Kamakura offers numerous temples, shrines and other historical monuments. In addition, Kamakura's sand beaches attract large crowds during the summer months.
4) Osaka
With a population of 2.5 million people, Osaka is Japan's third largest city and is considered the second most important. It has been the economic powerhouse of the Kansai region for many centuries.
5) Hiroshima
Hiroshima is the capital of Hiroshima Prefecture and the largest city of the Chugoku Region, the westernmost region on Japan's main island of Honshu. It is home to about one million people.
On August 6, 1945, Hiroshima was chosen by US armed forces as the first ever target of an atomic bomb employed over a populated area. As a result, 200,000 civilians lost their lives, and Hiroshima became a city vehemently engaged in the promotion of peace.
Hiroshima's Peace Park including the memorial museum, and the island of Miyajima (literally: shrine island), located 40 minutes from the city center by train and ferry, are among Japan's most interesting tourist attractions.
6) Yokohama
With a population of over three million people, Yokohama is Japan's second largest city. It is located less than 30 minutes south of Tokyo by train, and is the capital city of Kanagawa Prefecture.
Towards the end of the Edo Period (1603-1867), during which Japan isolated herself from the rest of the world, Western nations forced the country to open its ports to foreign trade. In 1859, Yokohama's port became one of the first ports to be opened, and Yokohama quickly grew from a small fishing village into one of Japan's major cities.
7) Nara
Japan's first permanent capital was established in the year 710 at Heijo, the city now known as Nara. As the influence and political ambitions of the city's powerful Buddhist monasteries grew to become a serious threat to the government, the capital was moved to Nagaoka in 784.
Nara is located in the Kinai plain, less than one hour from Kyoto and Osaka. Due to its past as the first permanent capital, it remains full of historic treasures, including some of Japan's oldest Buddhist temples.
8) Nikko
Located along Japan's Romantic Road, Nikko is a small city at the entrance to Nikko National Park. It is most famous for the Toshogu, Japan's most lavishly decorated shrine complex and mausoleum of Tokugawa Ieyasu, the founder of the Tokugawa shogunate.
Nikko has been a center of Shinto and Buddhist mountain worship for many centuries, and Nikko National Park continues to offer scenic, mountainous landscapes, lakes, waterfalls, hot springs, wild monkeys and hiking trails.
Nikko and the area around Lake Chuzenji, in particular, are well known for their beautiful autumn foliage (koyo). The best time to view the leaves depends on the elevation and year: For Yumoto and Lake Chuzenji it is usually mid October and for central Nikko early to mid November.
9) Takayama
Takayama is a town in the mountains of Gifu Prefecture which has retained a traditional touch like few other Japanese cities. It gained importance as the source of high quality timber and highly skilled carpenters. The Takayama Festival held in spring and autumn is considered one of Japan's three best festivals.
10) Kanazawa
Now the capital of Ishikawa Prefecture, Kanazawa's importance grew in the 15th century, when the powerful and militant Ikko sect established its new headquarters there after being chased out of Kyoto by the monks of Mt. Hiei.
During the Edo Period, Kanazawa was the seat of the Maeda clan, the second most powerful clan after the Tokugawa in terms of rice production and fief size. Accordingly, Kanazawa grew to become a town of great cultural achievements, rivaling Kyoto and Edo (Tokyo).
In World War Two, Kanazawa was Japan's second largest city (after Kyoto) to escape destruction by air raids. Consequently, parts of the old castle town, such as samurai, temple and pleasure districts, have survived in pretty good condition.
Sources
http://www.japan-guide.com/list/e1247.html
http://www.japan-guide.com/e/e623.html