What is the capital of Japan?

Tokyo's rise begins as Edo, a castle town that became the seat of the Tokugawa shoguns from 1603. For over two and a half centuries real power sat there while the emperor remained in Kyoto, so Japan effectively had a ceremonial capital and an administrative one. When the shogunate fell in 1868 and imperial rule was restored, the young Meiji emperor moved east to Edo, which was renamed Tokyo, meaning eastern capital, and took up residence in the shogun's castle. No law was ever passed formally transferring the capital, which is why purists occasionally argue about the status of Kyoto, but in every practical sense the government, the court and the machinery of the modern state relocated and stayed. The city has been rebuilt twice within living memory of its own records, after the great earthquake of 1923 and again after wartime destruction, which is part of why so little of old Edo survives above ground.

The imperial palace in Tokyo occupies the grounds of Edo Castle, so the emperor lives inside the shogun's old fortifications.