Ignace Murwanashyaka, the leader of the FDLR rebel group, and his aide Straton Musoni were held on suspicion of crimes against humanity and war crimes.
FDLR leaders fled to DR Congo after the Rwanda genocide in which some 800,000 people - mostly ethnic Tutsis - died.
The FDLR's presence in DR Congo has been at the heart of years of unrest.
The arrests come as UN peacekeepers continue to help the Congolese army battle the FDLR (Democratic Forces for the Liberation of Rwanda).
The operation has been underway since January but the FDLR remains active.
