Dias Kadyrbayev and Azamat Tazhayakov, both 19, stand accused of obstructing justice with the intent of impeding the investigation into the April 15 attack that left three dead and scores injured.
They had previously been accused of conspiracy to obstruct justice, a charge that remains in place, the US attorney's office in Boston said in a statement.
No date for a court appearance was disclosed.
If convicted, Kadyrbayev and Tazhayakov could face up to 20 years in prison and the prospect of deportation from the United States.
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Prompted by a text message from Dzhokhar Tsarnaev to go to his college dormitory room "and take what's there," Kadyrbayev and Tazhayakov -- together with a third conspirator -- removed a laptop computer, fireworks and other items.
They then allegedly took the items to their apartment in New Bedford, Massachusetts, where the items were subsequently stuffed into a garbage bag then put in a dumpster outside, the US attorney's office said.
Tamerlan Tsarnaev was killed amid a shootout with police later that night, while his younger brother -- who has pleaded not guilty to 30 counts including murder -- was later arrested hiding inside a small boat.