At a press conference on Tuesday, US federal prosecutor Preet Bharara called the scheme "securities fraud on cyber-steroids".
Twelve institutions were victims of the hacking, including JPMorgan, and asset manager Fidelity.
US prosecutors said they were expanding charges against two Israeli men, Gery Shalon and Ziv Orenstein, as well as a US citizen, Joshua Samuel Aaron.
Charges against the three men were expanded to include computer hacking and identity theft among 21 other counts.
`Criminal conglomerate`
"The charged crimes showcase a brave new world of hacking for profit," said Preet Bharara the lead prosecutor on the case.
"It is no longer hacking merely for a quick payout, but hacking to support a diversified criminal conglomerate," he said.
Mr Aaron, 31, was a fugitive and believed to be living in Moscow.
Mr Shalon, 31, and Mr Orenstein, 40, are in custody in Israel, where their lawyers couldn`t immediately be reached for comment.
The men allegedly manipulated stock prices by selling shares of companies to individuals whose contact information they had stolen. They then dumped their own shares, causing the price to fall.
The men were also charged with running an illegal payment processing business that they used to collect $18m (£11.9m) in fees.
Prosecutors claim the men hacked into competitors` systems to spy on them and then hacked into a credit card company investigating their payment processing business in order to avoid detection.
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