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.
BBC