Habyarimana Mucebo, a senior member of the Rwandan FDLR rebel group, was captured in Rutshuru, north-eastern DR Congo.
Members of the FDLR fled into DR Congo after the 1994 genocide in Rwanda.
The slaughter of some 800,000 ethnic Tutsis and moderate Hutus sparked years of unrest in the region.
Mr Mucebo, the FDLR intelligence chief, has been taken into custody for interrogation, the army says.
Most senior figures of the group are wanted by Rwanda for their alleged role in the 1994 killings.
Mr Mucebo's arrest is not linked to genocide charges as initially reported.
Congolese officials accuse him of links to atrocities blamed on the FDLR.
For many years, the Hutu rebel group had become a source of instability in DR Congo's North Kivu province.
Rwanda has sent troops and militias into DR Congo on several occasions since the genocide, saying they were going after the FDLR.
A Rwandan Hutu rebel commander wanted for atrocities committed on Congolese soil has been arrested in eastern Democratic Republic of Congo.