The UN-backed Special Tribunal for Lebanon (STL) submitted the long-awaited indictment without releasing names of those accused, but it is widely speculated that it names the Hezbollah rebel group.
Hariri was killed in February 2005, along with 22 others, when a massive car bomb exploded next to his motorcade in Beirut.
"The prosecutor of the tribunal has submitted an indictment and supporting materials to the pre-trial judge," STL said in a statement from Leidschendam, near The Hague.
In expectation of being named, Hezbollah warned on Sunday it would defend itself.
"We will not allow our reputation and our dignity to be tarnished nor will we allow anyone to conspire against us or to unjustly drench us in Hariri's blood," Hezbollah chief Hassan Nasrallah said in a televised speech.
Citing the UN-backed probe the Shiite rebel group withdrew from the Lebanese cabinet with its allies on Wednesday, prompting the collapse of the unity government led by Western-backed Prime Minister Saad Hariri, son of the murdered former premier.
US President Barack Obama welcomed Monday's indictment as “an important step toward ending the era of impunity for murder in Lebanon”, but urged calm amid rising tensions.
Hezbollah, "Party of God" in Arabic, has warned it would "cut off the hand" of anyone who tries to arrest any of its members over the Hariri killing, raising fears of renewed Sunni-Shiite sectarian violence, 20 years after the end of a 15-year civil war.