Seleka rebels control parts of northern Central African Republic where the LRA has been active
Dominic Ongwen, a senior commander in the rebel Lord’s Resistance Army (LRA), was taken into US custody this week.
The US had offered up to $5m (£3.3m) as a reward for information leading to his arrest, transfer or conviction.
A Seleka commander said he was captured after a 25-minute battle, after which they informed US forces in the area.
A US official had said that Mr Ongwen had defected, before being handed over to their forces.
Seleka plunged CAR into months of lawlessness when they seized the capital, Bangui, in 2013.
Ugandan officials say Mr Ongwen will be transferred to their custody in the coming days.
Known as the “White Ant”, he is considered by some to be a deputy commander to LRA chief Joseph Kony and is wanted by the International Criminal Court (ICC) for war crimes and crimes against humanity.
The LRA has abducted thousands of children in northern Uganda, and neighbouring countries, forcing the boys to become fighters and the girls to become sex slaves.
‘Really upset’
Mounir Ahamat, Seleka’s second-in-command in the region of Sam-Ouandja in north-western CAR, told BBC Afrique that a US army helicopter had gone to collect Mr Ongwen after the battle.
He said that, apart from the reward money, Seleka was disappointed that the US had not publicly recognised their role in the arrest of Mr Ongwen.
He said that they had reinforced their fighters on the ground in order to find him.
“If they don’t give us that money, they could at least say it’s thanks to us they were able to get this lieutenant colonel. Not only they did not give us the money, but they didn’t recognise what we have done in the field,” he said.
“I am really upset by it.”
Explaining the circumstances of the capture, he said that as the US helicopter approached, the LRA commander had asked if it was Ugandan because “they would kill him”.
Seleka forces have withdrawn from the CAR capital but they still control many northern areas of the country.
Of the top five LRA commanders for whom the ICC issued arrest warrants, only two – Joseph Kony and Okot Odhiambo – remain at large.
The Ugandan government has said it would prefer Mr Ongwen to face justice at home, despite originally requesting the ICC to investigate the LRA.
But Uganda’s President Yoweri Museveni has been very critical of the ICC recently, accusing it of unfairly targeting African leaders.
The LRA rebellion began more than two decades ago in northern Uganda and its estimated 200-500 fighters have since terrorised large swathes of the Democratic Republic of Congo, South Sudan and the CAR.
The US first deployed about 100 special forces in 2011 to support thousands of African troops searching for LRA commanders.
