The charges against Javier Martin-Artajo and Julien Grout allege they tried to hide millions of dollars.
They are accused of keeping false records on the trades and committing wire fraud.
The bank suffered the multi-billion dollar loss after trades made by the so-called London Whale went bad.
The US Department of Justice alleges that Mr Martin-Artajo, who was responsible for JP Morgan's trading strategy in London, and Mr Grout, who submitted the trades, "artificially increase[d] the market value of securities to hide the true extent of hundreds of millions of dollars of losses".
The complaint, which was unsealed on Wednesday in a federal court in Manhattan, goes on to say that the two were responsible for hiding more than half a billion dollars in losses.
Mr Martin-Artajo and Mr Grout have denied the charges.
"Mr. Martin-Artajo is confident that when a complete and fair reconstruction of these complex events is completed, he will be cleared of any wrongdoing," said Norton Rose Fulbright, the law firm representing Mr Martin-Artajo.
Terrible trade
The London-based derivatives trader Bruno Iksil, who earned the nickname the "London whale" for his big bets on financial derivatives markets, has not been charged.
He is cooperating with the authorities, according a separate agreement also released on Wednesday but dated 20 June.
Mr Iksil "has several emails in which he tells his superiors that the losses are getting horrific that he can't keep hiding it anymore", Columbia University professor John Coffee told the BBC.
"That is exactly contrary to the intent you would need for securities fraud."
"Remember it's not a crime to make a terrible losing trade."
JP Morgan boss Jamie Dimon said at the time of the loss in May 2012 that the trade was "the stupidest and most-embarrassing situation I have ever been a part of".
Mr Dimon has not been charged with any wrongdoing.
JP Morgan is also under investigation by the US Securities and Exchange Commission for possible failure to enact sufficient internal controls to stem the loss.
Source: BBC
