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Police alleged the two ordered employees to drop to the floor as they demanded money.
"Both suspects got away with thousands of dollars. That incident was also planned by this manager," said Jim Amormino, Orange County Sheriff's Department.
Authorities say the Rite Aid manager was Cynthia Johanna Ongamsina-Jenkins. The robberies happened more than a year and a half ago.
Investigators suspect that the 43-year-old also helped fake her own robbery in Dana Point last month. She was working as a manager at another Rite Aid and was carrying the store deposits to the bank when two masked men, matching the same description as before, approached her.
"She was approached by two male African Americans armed with handguns and they robbed her of the money. They took approximately $20,000," said Amormino.
Ongamsina-Jenkins reported the alleged robbery to the sheriff's department.
"Investigators met with the manager and determined that the manager had set up the entire robbery," said Amormino.
Authorities say that Ongamsina-Jenkins served prison time in the 1990s for solicitation for murder for hire. As investigators search for her two alleged accomplices in the recent cases, Ongamsina-Jenkins now faces a number of new felony charges including grand theft and robbery.