The filmmaker from San Diego, California has been charged with one count of causing USD 20,000 in illegal campaign contributions to be made to a candidate for the US Senate in 2012, Manhattan's India-born prosecutor Preet Bharara said.
The charge carries a maximum sentence of two years in prison.
The 52-year-old filmmaker is also charged with one count of making false statements to the Federal Election Commission in connection with the illegal campaign contributions, which carries a maximum sentence of five years in prison.
In announcing the indictment, Bharara said his office and the FBI have a "zero tolerance approach to corruption of the electoral process. If, as alleged, the defendant directed others to make contributions to a Senate campaign and reimbursed them, that is a serious violation of federal campaign finance laws."
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FBI Assistant Director-in-Charge George Venizelos said D'Souza finds himself on the wrong side of the law since trying to influence elections through bogus campaign contributions is a serious crime.
The documentary had equated reelection of Obama with the death and dismemberment of the US and had been running at number three on the top movies list when it was released.
D'Souza's lawyer said in a statement quoted by New York Times that his client did not act with any corrupt or criminal intent.
The Senate candidate was not identified in the indictment.
A report in the NYT said D'Souza had donated to only one federal candidate in 2012, giving USD 5,000 to Wendy Long, a New York Republican who lost her challenge to democratic Senator Kirsten Gillibrand.
According to the allegations in the indictment, the Election Act had in 2012 limited both primary and general election campaign contributions to a total of USD 5,000 from any individual to any one candidate.