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According to a human rights activist, the Gunman shot Sheikh Ali Amini during evening prayers on Saturday and then fled.
The cleric was a strong critic of Islamic militancy in the region Africa Today News, New York can confirm.
Eastern DR Congo has been badly hit by instability, including attacks claimed by the Islamic State (IS) group.
Many armed groups operate in eastern DR Congo, a legacy of the conflicts that gripped the region in the 1990s.
BBC World Service Africa editor Will Ross says Sheikh Amini’s killing during the Muslim holy month of Ramadan has caused a great deal of shock in Beni, a city with a population of about 200,000.
A prominent human rights activist in Beni, Stewart Muhindo, said this was the first such killing in the city.
‘It happened at 19:15 during evening prayers. Shots were fired inside the mosque hitting the imam. The gunman got away as he had an accomplice outside the mosque waiting with a motorbike,’ Mr Muhindo told the journalists.
While it is unclear who was behind the attack, much of the violence in the area is carried out by a Muslim rebel group, the Allied Democratic Forces (ADF), our correspondent says.
IS has taken credit for some ADF attacks, but it is unclear how strong the links are between the two groups.
AFRICA TODAY NEWS, NEW YORK