The two men have been identified as Dias Kadyrbayev, 19, and Azamat Tazhayakov, 19. Both suspects were college friends of Dzhokhar Tsarnaev but did not play a direct role in the attacks.
Kadyrbayev and Tazhayakov had originally been charged with conspiracy to obstruct justice on May 1 via criminal complaint.
The suspects were residing in New Bedford on student visas and were held in jail for more than a week in May on allegations that they violated their visas while attending UMass.
The indictment alleges the suspects destroyed or concealed a laptop computer and a backpack containing fireworks belonging to Dzhokhar after receiving a text message from the suspect.
Kadyrbayev and Tazhayakov allegedly agreed to place Tsarnaev's backpack in a garbage bag and in a trash dumpster outside their New Bedford apartment. The backpack was later found in a landfill by law enforcement officers.
If they are convicted, both face up to 20 years in prison on the obstruction of justice count and up to five years in prison on the conspiracy county. Both face the possibility of being deported.
The twin blasts at the Boston Marathon on April 15 killed three people and wounded 170 others. According to the FBI, about a month before the bombing, Dzhokhar Tsarnaev told Tazhayakov and Kadyrbayev that he knew how to make a bomb.
Brothers Tamerlan and Dzhokhar Tsarnaev were named suspects based on surveillance footage. Tamerlan was killed in a shootout with police days later, while Dzhokhar was captured alive following a massive manhunt.
The Associated Press contributed to this report.