Maria Dionisio of Pacifica and Hannah Yau of Fremont are accused of stealing $2.6 million from British-based Autonomy Software at its San Francisco office.
The DA says both were responsible for processing payroll and gave themselves unauthorized bonuses.
"There was a bonus check written to one of them for $98,000 and I think it's important to note that their base salary was $63,000," Kamala Harris said.
Investigators are trying to account for all the money and are currently freezing the defendants' accounts.
Both face about six years in prison.
