Head of the Corsica Nazione nationalist party, Jean-Guy Talamoni was taken into custody on Thursday.
One of Corsica's best-known politicians, Talamoni had been seen as a key player in government efforts to end decades of separatist violence and mafia crime on the Mediterranean island.
But a judicial source said he was arrested as part of a criminal investigation into another leading nationalist, Charles Pieri.
The authorities have cracked down on the mafia gangs, which the government says have close links with nationalist circles.
The probe into Pieri, who was convicted in 2000 on arms offences, involves alleged malpractices surrounding the Bastia football club in northern Corsica during the 1990s.
Criminals or separatists?
Paris accuses the island's mafia gangs of flooding the local economy with dirty money and running criminal gangs.
Corsica saw a fresh upsurge in violence last year after the arrest of the chief suspect in the 1998 killing of the French government's top official in Corsica.
Police offices and holiday villas belonging to non-Corsicans were attacked.
Corsican nationalists have since announced a truce.
But government policy on how to deal with the island is still unclear after residents rejected an offer by Paris of limited autonomy in a referendum last July.