Gonzales is alleged to have operated under three pseudonyms, hacking through network firewalls (protection software) along with two un-named co-conspirators, the justice department said.
The three individuals are suspected of sending the data they stole to computer servers in California, Illinois, Latvia, the Netherlands and Ukraine. The alleged crimes stretch back to October 2006.
They used hacking techniques to cover their tracks and avoid detection by anti-virus software used by the companies they targeted, the indictment alleges.
If he is convicted, Gonzales could be jailed for up to 20 years on the wire fraud conspiracy charge and an extra five years in prison on the conspiracy charge.
He could also face a fine of $250,000 for each charge if he is found guilty.
Gonzales, who is in federal custody, was charged in May 2008 by authorities in New York for his alleged role in the hacking of a computer network run by a national restaurant chain.
He is expected to face a court to answer the charges next month.