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What's the difference between marking a comment as spam and trashing it?

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Well, for one thing, if you have Akismet running, marking a comment as spam will tell Akismet and it'll use that comment to learn what to mark as spam automatically. –  John P Bloch Sep 28 '10 at 14:03
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up vote 3 down vote accepted

In vanilla WordPress the only difference is that trashed comments get deleted automatically after (customizable) time span.

Adding plugins to the picture - it might make difference to what/how specific plugin learns from incoming spam.

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