How did Professor McGonagall know Ginny Weasley was the one taken into the chamber of secrets?

Answer 1

Professor McGonagall knew Ginny was taken in because she wasn't seen for long and when the message "Her body will lie in the chamber forever" came, she was the only Gryffindor who wasn't anywhere in the dormitory

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Answer 2

It is never actually explained how Professor McGonagall knew that Ginny Weasley was the one taken. Due to the attacks the school was being very strict about security, so it is likely Ginny was the only student unaccounted for on the class registers.