The two Saudis and one US citizen allegedly worked together to unmask the ownership details behind dissident Twitter accounts on behalf of the government in Riyadh and the royal family, the department said.
According to a court filing, they were guided by an unnamed Saudi official who worked for someone prosecutors designated "Royal Family Member-1," which The Washington Post reported was Saudi Crown Prince Mohammed bin Salman.
Those charged were former Twitter employees Ali Alzabarah and Ahmad Abouammo, along with Ahmed Almutairi, a marketing official with ties to the royal family.
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"The criminal complaint unsealed today alleges that Saudi agents mined Twitter's internal systems for personal information about known Saudi critics and thousands of other Twitter users," said US Attorney David Anderson.
"US law protects US companies from such an unlawful foreign intrusion. We will not allow US companies or US technology to become tools of foreign repression in violation of US law," he said in a statement.
The lawsuit comes as US-Saudi relations continue to suffer strains over the brutal, Riyadh-sanctioned murder last year of Saudi journalist Jamal Khashoggi, who wrote for, among others, The Washington Post.
A critic of Crown Prince Mohammed, Khashoggi was killed and dismembered inside the Saudi consulate in Istanbul.
According to the Post, US intelligence has concluded that the prince himself was closely linked to the murder.
Abouammo, 41, an American, and Saudi national Alzabarah, 35, were recruited in 2014-2015 to use their positions in Twitter to gain access to private information related to the accounts of critics of Riyadh, the indictment says.
Saudi citizen Almutairi, 30, was a critical go-between who arranged contacts between the two others and the unnamed Saudi official.
The indictment said Almutairi controlled a social media marketing company that did work for a royal charity and members of the royal family, "including Royal Family Member-1."
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Abouammo was paid over $300,000 and received a Hublot watch worth more than $20,000 for his work.
Alzabarah's payment was not detailed, but the filing said he quickly fled the US with his family in December 2015 after Twitter management confronted him about his unauthorised accessing of user information for some 6,000 Twitter accounts, including accounts of known prominent dissidents and royal family critics.
All three are charged with acting as illegal agents of a foreign government, a charge that can indicate both illegal lobbying and espionage.
Abouammo was also charged with destroying, altering, or falsifying records related to a federal investigation.
"These individuals are charged with targeting and obtaining private data from dissidents and known critics, under the direction and control of the government of Saudi Arabia," said FBI Special Agent John Bennett.
"The FBI will not stand by and allow foreign governments to illegally exploit private user information from US companies."
The Justice Department said Abouammo was arrested on Tuesday in Seattle, Washington, but that both Alzabarah and Almutairi remain at large and are believed to be in Saudi Arabia.
Federal warrants have been issued for the arrest of both.
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