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I watched Tokyo Ghoul and I know that from season 2 it deviated from the manga, so I decided to read it and see the other version of Tokyo Ghoul. But I don't want to start from the beginning as it's almost the same, so I want to know which chapter was the first one in which the manga and the anime were different.

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If you don't want to read from the beginning, start from Chapter 67 if you finished watching the first season.

This is the first chapter adapted by the first episode of the second season, and as you mentioned, the second season deviated entirely from the manga. Some arcs were altered or only partially shown, starting from the Post-Aogiri Tree/Timeskip Arc.

However, as mentioned by the people here, if you are planning on reading the manga, I highly recommend you start from the beginning. It might seem tedious but there are a lot of things not included in the anime. It might be an understatement to say you are missing half the experience of Tokyo Ghoul if you do not read the manga from the start.

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