The French Armed Forces ministry said Oumeya Ould Albakaye was captured by Operation Barkhane forces between the night of June 11 and the early hours of June 12 close to the border between Mali and Niger.
Souring relations between France and the military junta in its former colony of Mali have led France to withdraw troops that were deployed in 2013 to push back militants linked to al Qaeda, and later to Islamic State.
As France withdrew its forces, Bamako brought in the Russian mercenary Wagner Group to bolster protection for Mali's regime. Wagner Group has been accused of significant human rights violations in numerous places in Africa.
Mali has been hit by violence since 2012 when jihadists took over the north. France beat them back, but by 2015 they had regrouped and unleashed a wave of attacks in the centre. They have since spread into Niger and Burkina Faso, raising concerns about regional instability.