At the time, it said Ms Holmes would remain on the board of the company.
Theranos announced Friday that Holmes was resigning as CEO.
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Although Theranos claimed its "miniLab" blood analyzer could perform a full range of tests, Holmes and Balwani knew their analyzer "had accuracy and reliability problems, performed a limited number of tests, was slower than some competing devices, and could not compete with larger, conventional machines in ... the simultaneous testing of blood from many patients", the indictment says.
The two face up to 20 years in jail, plus a maximum fine of about $2.75 million each.
It also alleges that the pair defrauded doctors and patients by making false claims about the effectiveness of Theranos's blood tests, including those for calcium, potassium, HIV and diabetes.
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They charged Ms Holmes, 34 and Mr Balwani, 53, with wire fraud. Known within Theranos as a mercurial and easy-to-anger manager, he left the company in 2016, as the company's troubles were building amid sanctions from federal regulators and a darkening storm of bad press. But Balwani, the company's longtime COO and Holmes's ex-boyfriend, is a more shadowy figure, with virtually no online trace.
"This district, led by Silicon Valley, is at the center of modern technological innovation and entrepreneurial spirit; capital investment makes that possible", Tse said in a statement. The company has repeatedly laid off employees in an effort to cut costs and is staring down debts that could force it to liquidate as early as this summer, the Wall Street Journal has reported. She paid a $500,000 penalty, returned millions of shares to the company and relinquished her company voting power under the terms of the settlement.
Elizabeth Holmes is no longer running Theranos, the company that promised a portable blood analyzer that could have changed blood testing, if it had been what the company promised.
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The company did not immediately respond to a message seeking comment on Friday's indictments.