I have the Jr rail pass which will let me use the yamanote line for free in Tokyo . Should I still get the pasmo card ? Will also be in Kyoto and hakone
You don't "need" a Pasmo card - you can use cash just fine. The card can be convenient though, and save wear and tear on your pockets. There are limitations, though. See this page: http://www.japan-guide.com/e/e2359_003.html
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http://www.japan-guide.com/e/e2359_003.html