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From dexter.wikia: "The flashbacks end after Season Two and Harry remains as a part of his subconscious helping him survive and make the right decisions. It is unknown if this could actually be Harry's spirit, as Dexter's mother Laura also appears to him and even his own brother Brian for a short while. Harry always acts indifferent and with a calm understanding, despite Dexter's situation."
The first season is close to the book, but the end changes everything, then you can read book and watch the series without one spoil the other. The series use some elements from the others books, but the story is different..