His killing is the latest blow to the FDLR, which has been weakened in recent years by arrests of several of its leaders and military pressure from Democratic Republic of Congo's armed forces, the FARDC, and other militias.
The army "neutralised another radical leader of the FDLR on Saturday the ninth of November at 14:00," said Guillaume Njike, a Congolese army spokesman.
Musabimana, who was also known by his nom de guerre Jean-Michel Africa, was killed alongside four of his bodyguards following an intense firefight in Binza, North Kivu, near the Ugandan border, Njike added.
Congolese forces killed the leader of the main branch of the FDLR, Sylvestre Mudacumura, on Sept. 18.
The group split in a row over ranks and money in 2007, said Christoph Vogel, a researcher at the conflict research programme hosted by the London School of Economics and Ghent University.
"Compared with Mudacumura, (Musabimana) is a small fish so I doubt this is as significant, but it shows that different actors seem to be converging on a more coordinated push against FDLR and anything they define as such."
Rwanda's foreign affairs minister Olivier Nduhungirehe said Musabimana's fighters were responsible for a deadly cross-border attack in October in a mountainous region famous for its mountain gorillas in which eight people died.
"This is an act of justice," he told Reuters by telephone.
"This is the confirmation of the resolve of (Congolese) President Félix Tshisekedi and the FARDC to eradicate armed groups and terrorist organizations in eastern Congo. We thank them for that."
The FDLR has also been a source of friction between Rwanda and Uganda in the last year. Rwanda accused Uganda in March of supporting the FDLR and another Congo-based rebel group opposed to the Rwandan government. Uganda denied the allegations.
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