Spokeswoman Staci Slaughter said the wooden plaque marked the spot on a brick wall above right center field near the bleachers where Bonds had hit his record-breaking 756th home-run ball on Aug. 7, 2007.
"We're getting it replaced," Slaughter said.
She said items get taken from the stadium often, and that a new plaque will go up shortly.
The plaque was installed in 2008 and had been there ever since, Slaughter said. It was high up on the wall, and it remains unclear how someone got to it and removed it.
She said the ball club is reviewing surveillance footage to find any clues about the plaque's disappearance, but that police are not getting involved.
