The Kinshasa Government hopes that the International Court of Justice (ICJ) will order an "immediate and unconditional withdrawal" of Rwandan and rebel troops from Congolese territory.
The ICJ, which can take up to four years to issue rulings, has said it will examine the case as early as 13 June.
The recent death of up to 250 people in Kisangani was the latest event in a complex war which has engulfed the Congo since 1998, drawing in the armies of six other countries which have fought over Congolese mineral resources.
"In killing, massacring, raping, throat-slitting and crucifying, Rwanda has rendered itself guilty of the genocide of more than 3.5 million Congolese people," says the case filed before the court in The Hague.
List of woes
Independent estimate put the death toll from fighting, famine and disease at two million.
Kinshasa's suit also cites cases of assassination, kidnapping, systematic looting, inhuman and degrading treatment, as well as the destruction of the country's flora and fauna.
It urges the court to declare that Rwanda is in violation of the UN Charter and the International Charter on Human Rights.
"Failing to order the requested measures at once would have irreparable consequences," the suit reads.
Kinshasa has already filed a complaint against Uganda, Rwanda and Burundi before the ICJ, but it had to withdraw its case because the authorities in Kigali and Bujumbura had not recognised the court's jurisdiction.
Martyr town
"We have decided to start new proceedings because of the events in Kisangani," Congolese Foreign Minister Leonard She Okitundu told the BBC's French service.
He said that "crimes could not go unpunished", and that measures should be taken to protect the people of the rebel-held town.
Eye-witnesses say that rebel "death squads" executed scores of people suspected of supporting an uprising against the rule of the Rwandan-backed Rally for Congolese Democracy (RCD).
Mr Okitundu criticised the RCD for not withdrawing from Kisangani, as required by a United Nations Security Council resolution on the demilitarisation of the city.
The killings in Kisangani took place a few weeks after the government of President Joseph Kabila signed a peace deal with some rebel groups, but not the RCD.
Jean-Pierre Bemba, from the Ugandan-backed Movement for the Liberation of Congo, is set to become the new prime minister in a political deal reached in South Africa.
Zimbabwe and Angola have troops in DR Congo, backing Mr Kabila.