There was a heavy police presence around the town hall following the arrests of Gultan Kisanak and Firat Anli, who together lead a city that has been rocked by clashes between security forces and members of the outlawed Kurdistan Workers' Party (PKK).
Dozens of police were surrounding the town hall with light armoured vehicles and trucks loaded with water cannon as officers searched the building, an AFP correspondent said.
Kisanak was held at the local airport and Anli at his home, officials told AFP.
Last month, 24 mayors suspected of links to the PKK were suspended and replaced with officials close to Erdogan's ruling Justice and Development Party (AKP).
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The controversial move sparked fresh clashes, with one of the new administrators shot dead in Van, eastern Turkey, on October 16.
More than 40,000 people have been killed since the PKK first took up arms in 1984 demanding an independent state for Kurds. Since then the group has narrowed its demands to greater autonomy and cultural rights.