Azamat Tazhayakov and Dias Kadyrbayev are accused of conspiring to obstruct justice.
A third man, Robel Phillipos, is accused of making false statements to federal investigators.
An FBI affidavit says the three men removed bombing suspect Dzhokhar Tsarnaev's backpack from his dorm room at the University of Massachusetts in Dartmouth three days after the bombing.
The affidavit says Tazhayakov and Kadyrbayev agreed to get rid of it after concluding from news reports that Tsarnaev was one of the bombers.
The trio are due in court later today.
Three people were killed and more than 260 injured when two bombs exploded near the finish line on April 15.
Suspect Tamerlan Tsarnaev died after a gunfight with police several days later. His brother, Dzhokhar, was captured and is in a hospital prison.
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