Mr Murwanashyaka has lived in Germany for several years
Police in Germany have arrested two Rwandan militia leaders on suspicion of crimes committed in the east of the Democratic Republic of Congo.
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.
Ethnic Hutu, aged 46
Been in Germany since before Rwanda genocide
Denies charges his men are linked to genocide
Says fighting for democracy in Rwanda
Commands 5-6,000 men
FDLR said to smuggle gold from DR Congo to buy weapons
Accused of war crimes and crimes against humanity
Accused of killings, rape, looting and conscripting child soldiers in DR Congo
The FDLR is accused of funding its arms purchases by smuggling gold and other minerals from areas it controls in the North and South Kivu provinces, just across the border from Rwanda.
Mr Murwanaskyaka, 46, was arrested in the city of Karlsruhe, while 48-year-old Mr Musoni was held in the Stuttgart area, German prosecutors said in a statement.
The statement said that the pair were the leader and deputy leader of the FDLR.
"The accused are strongly suspected, as members of the foreign terrorist organisation FDLR, of committing crimes against humanity and war crimes," it said.
It added that "FDLR militias are believed to have killed several hundred civilians, raped numerous women, plundered and burned countless villages, forcing villagers from their homes and recruiting numerous children as soldiers".
Lobby group Human Rights Watch (HRW) has welcomed the arrests.
"Our research clearly indicates that Mr Murwanashyaka has a powerful influence over the FDLR militia who have deliberately targeted and killed hundreds of civilians in eastern Congo and that he is directly linked to the crimes," said HRW DR Congo expert Anneke Van Woudenberg.
Mark Doyle, BBC News
There is no doubt that Ignace Murwanashyaka has had direct command and control over some of the illegal mining activities of Rwandan rebels operating in eastern DR Congo.
I know, because when I travelled in the area earlier this year with a BBC team, it was he who gave us permission to enter the rebel mining strongholds in the South Kivu region.
I had sought permission from rebel officers on the ground. All of these officers declined to give us permission to enter their area until Mr Murwanashyaka agreed.
It was a public relations gaffe on the rebels' part, however, because we managed to prove, despite rebel denials, that they were deeply involved in illegal mineral mining.
"Mr Murwanashyaka's arrest on war crimes and crimes against humanity is a welcome step to bringing justice for these brutal crimes," she added.
Mr Murwanashyaka, an ethnic Hutu, has lived in Germany since before the 1994 genocide in Rwanda.
He has always denied that his men, believed to number 5-6,000, were involved in the genocide and says they are fighting to bring democracy to Rwanda.
He was among 15 people whose assets were frozen by the Security Council in 2005 on suspicion of involvement in war crimes in Rwanda or DR Congo.
The FDLR's presence in eastern DR Congo has led to years of fighting in the region, and Rwanda's Tutsi-dominated government has twice invaded, saying it is trying to wipe them out.
Some FDLR leaders have been accused of involvement in the Rwandan genocide.