Loughlin and her husband, Mossimo Giannulli, had previously been charged with conspiracy to commit mail fraud. The indictment adds a charge of money laundering against all 16 defendants.
The move comes a day after 14 other defendants, including 13 parents and one coach, agreed to plead guilty in the case.
Loughlin and Giannulli are accused of paying $500,000 to get their daughters admitted to USC as members of the crew team. According to the indictment, the couple paid $200,000 per child to the Key Worldwide Foundation, a fake charity set up by admissions consultant William Rick Singer. They paid an additional $50,000 per child directly to Donna Heinel, the senior associate athletic director at USC, prosecutors allege.
The money laundering charge relates to the payments to the foundation. Prosecutors allege that the charity was established to launder bribe payments, and some parents are accused of writing the payments off as a charitable deduction on their income taxes.
Bill McGlashan, a founding partner of TPG Growth, was also among the parents indicted on Tuesday. McGlashan is accused of paying $250,000 to get his son admitted to USC as a football recruit.
Actress Felicity Huffman was among the parents who agreed to plead guilty on Monday. Prosecutors are expected to seek a sentence of about four to six months for Huffman, while her attorneys are expected to seek a lower range or supervised release.
The U.S. sentencing guidelines heavily factor the amount of money involved in a crime, indicating that Loughlin and Giannulli could face substantially more time than Huffman if convicted. Under the guidelines, prosecutors could seek about 24-30 months in prison.
The Hallmark Channel cut ties with Loughlin after the scandal broke last month.