IMU members fought alongside the Taliban in Afghanistan but the group was largely destroyed by the US-led military campaign there in 2001.
The two were detained in 2001 by US forces in Afghanistan and held in the Guantanamo military prison in Cuba for five years before returning to Tajikstan to face charges of being mercenaries in a foreign country.
Tajikstan's foreign ministry says at least 10 Tajik citizens are being held in Guantanamo Bay, most of them detained by US troops in Afghanistan on suspicion of involvement with the Taliban or al-Qaeda.
In the last five years, around 70 suspected members of the IMU have been arrested in Tajikistan, a former member of the Soviet Union with a mainly Muslim population of seven million.
Most have been put on trial and received sentences of between 15 and 25 years.