The investigation comes as Turkey carries out its biggest operation in years against Kurdistan Workers Party (PKK) militants who have responded by tearing up a 2013 ceasefire and staging daily attacks against the security forces.
Those placed under arrest include the co-mayors of the central Sur district of the region's biggest city Diyarbakir, Seyid Narin and Fatma Sik Barut, the official Anatolia news agency reported.
It is common in Kurdish regions of Turkey for posts to be shared between a man and a woman to promote gender equality.
Anatolia said they had been charged with seeking "to break up the unity of the state and integrity of the country". It is not clear when the trial will start.
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All of them are members of the Democratic Regions Party (DBP), which has close ties to Turkey's main pro-Kurdish political force the Peoples' Democratic Party (HDP).
Turkish media reports said they had been initially detained on Wednesday as part of an investigation into moves by some Kurdish-dominated regions in Turkey to declare "self rule" since the latest crisis took hold.
Tensions are riding high in Turkey's southeast as the military presses on with its campaign against PKK militants both within the country and in their strongholds in northern Iraq.
According to figures published Saturday by the state-run Anatolia news agency, 812 PKK militants have been killed in the campaign while 56 members of the Turkish security forces have lost their lives.
It is not possible to independently verify the death toll for PKK militants. Turkish officials have vehemently denied claims that civilians have also been targeted.