Maria Lourdes B. Dionisio, 46, of Pacifica, and Hannah Yau, 56, of Fremont, are accused of fraudulently issuing themselves checks over a four-year period at Autonomy, Inc.
Dionisio was a payroll clerk and Yau a financial analyst at the company.
The women appeared in San Francisco Superior Court this morning for the first time since their arrests Wednesday. Their newly appointed attorneys pleaded not guilty on their behalf to charges of grand theft and embezzlement.
Both were ordered held on $1 million bail and are set to return to court Friday for further proceedings.
At a news conference Wednesday, District Attorney Kamala Harris said the women "essentially ended up being foxes that guarded the henhouse," padding their salaries with bonus checks amounting to about $1.3 million each.
The company began an investigation after Dionisio was fired for unrelated reasons in May, Harris said. She said that when Dionisio filed for unemployment insurance, she listed an annual salary of nearly $450,000, far more than her base salary of $63,000.
Dionisio is alleged to have drafted the checks. Prosecutors said Yau also received checks and failed to notify the company of the theft.
Prosecutors have charged Dionisio with grand theft, embezzlement and computer crimes, all felonies. Yau is charged with grand theft and embezzlement.
If convicted, Dionisio could face up to five years and eight months in prison and, with allegations of excessive taking, Yau could face up to six years and eight months in prison, according to the district attorney's office.