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Railroads
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Japanese Railway History
The East Japan Railway Culture Foundation publishes this series of articles on Japan’s railroad history.

Brief History of Japanese Railways
This is a timeline, with links to some images.

Locomotive to Bullet Train: A Railroad History of Modern Japan
I welcome the return of this detailed history, by way of the Internet Archive. Unfortunately the last section and the photographs are missing, but most of the text is still available. This is definitely the most detailed online reference on the subject.

Ichiban
The best Japanese railfan site I’ve found yet! Galleries of rolling stock, fare cards, and model railroads.

Kurogane no Michi
Great listing of rail resources from all over Asia. Lists of JNR steam rolling stock, operating lines, and even an old locomotive given new life as a cartoon hero!

Growth of the Japanese Railroad System
Academic paper on Japanese rail history, still available on the Internet Archive.