"Souleymane Keita, the top jihadist leader in the south of the country, was arrested a few days ago on the Mauritanian border, and transferred to Bamako on Wednesday," a security source said.
Another security source said the arrest, near the town of Sokolo, followed the capture of one of his allies a few months ago in the centre of the country.
"He was about to head to Timbuktu, probably to meet up with his mentor Iyad Ag Ghaly in the Kidal region" in north-east Mali, the source said, referring to the Tuareg leader of the Islamist Ansar Dine group.
But when French troops stepped in to oust the Islamists in January 2013, Keita headed south to his native region to set up a new group, the Khaled Ibn al-Walid "katiba", meaning combattant unit.
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The group, also known as "Ansar Dine of the South", has some 200 fighters, a Malian security source said.
In March 2015, security services accused him of heading a jihadist military training camp discovered outside Bamako.
Keita was also accused last year of attacks in Fakola and Misseni near the Ivory Coast border and of "terrorist attacks" in the capital.