Looks like Karl Rove was Matt Cooper's source about Valerie Plame. But he may not have known her name or that she was undercover at the time.
The Washington Post confirms that Mark Felt is Deep Throat. Woodward, Bernstein, and Ben Bradlee confirmed the story as well. Woodward is writing an article about the experience to be run on Thursday.
Identity of Deep Throat finally revealed. Mark Felt, who was second in command at the FBI at the time, helped Woodward and Bernstein with their research into Watergate.

