The huge data breach impacted at least 500mln Yahoo! email accounts, including those of Russian and US officials, Russian journalists and various business men and women.
The indictments, announced in a press conference on Wednesday evening, target two members of the Russian intelligence agency, FSB, as well as two other hackers allegedly hired by the Russians.
The charges brought against FSB officers Dmitry Dokuchaev and Igor Sushchin, as well as criminal hackers Alexseyevich Belan and Canadian-born Karim Baratov, include hacking, wire fraud and trade secret theft.
The indictments are unrelated to the reported hacking of the Democratic National Committee during the 2016 presidential campaign, the DoJ said.
The United States doesn’t have an extradition treaty with Russia, so unless the alleged hackers either give themselves up or accidentally visit a country which would transfer them to the US, the four men are unlikely to face further action.
Instead, the DoJ said taking steps such as charges and imposing sanctions can act as a deterrent.
At that time, it was thought to be the biggest data breach in history, although Yahoo! quickly topped its own record when it revealed that more than 1bn user accounts had been hacked in 2013.
Shares in Yahoo! gained 0.3%, or US$0.13, to US$46.40.