Toward the end of my last stay in Tokyo, I wound up helping an American serviceman find his way to Ueno and the Keisei Skyliner while we were on the Yamanote (The Skyliner is a waaay cheaper way to get to Tokyo from Narita, best if u dun have an expense account or a JR Pass).
He was a bit flustered as he ran in the car (getting his arm caught in the door in the process). Seems that he was trying to get to Narita and got the JR (Japan Rail) and the Tokyo Metro mixed up.
The JR usually runs above ground. The Yamanote and the Chuo are JR Lines.
The Tokyo Metro generally runs underground, although as you head further away from the Yamanote, some Metro lines become elevated. To make things even more confusing, the majority of the Metro lines were once part of the Eidan, a privately run subway system. The remainder were Toei Lines, which was owned by the Tokyo Metropolitan Government. All these lines are known as the "Tokyo Metro", but the fare structures are slightly different between the two subsystems.
Transferring about can be a challenge if you're not competely familiar with the city (as I'm not, at least not yet!). I found this link for a site run by Tokyo Metro that helps you transfer between the two subway systems.
Neat, wish I knew about this site before I left!
Hat tip to Mari for the Tokyo Subway Transfer link!

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