The Tuareg separatist group MNLA says it arrested Mohamed Moussa Ag Mohamed and Oumeini Ould Baba Akhmed on Saturday near Mali's border with Algeria.
Ag Mohamed is the number-three leader of Ansar Dine and helped impose a harsh form of Islamic law on the city of Timbuktu.
Baba Akhmed is believed to be a member of the Movement for Unification and Jihad in West Africa, also known as MUJAO.
The two groups along with al-Qaida in the Islamic Maghreb controlled the major towns of northern Mali for about nine months before being driven out by the French and Malian armies.
French Foreign Minister Laurent Fabius said Monday that French warplanes were continuing bombing raids on supply routes and training centers in the remote desert of northeastern Mali. He told French radio that the objective is to make it impossible for the rebels to stay in northern Mali long-term.
Also Monday, U.S. Vice President Joe Biden met with French President Francois Hollande in Paris and praised the French operation in Mali, calling it "decisive."
Biden also backed France's call for U.N. peacekeepers to be deployed to Mali
President Hollande is pushing for African forces to take over for French troops that have been battling the militants for the past three weeks.
Mr. Hollande made a one-day visit to Mali on Saturday, making brief stops in Sevare, Timbuktu and the capital, Bamako.
He told a cheering crowd in Bamako that French forces are fighting so people in Mali, a former French colony, can live in peace and have democracy.
Mali was plunged into crisis last year when soldiers overthrew the president, allowing the MNLA and Islamist groups to take control of the north. The Islamists then seized full control of the region and imposed strict Sharia law with measures that included a ban on music and forcing women to wear veils.
The groups also carried out public executions, floggings, and amputations for alleged criminals, drawing strong condemnation for human rights groups and the United Nations.