Selahattin Demirtas was detained at his home in the southeastern city of Diyarbakir while the co-chairperson Figen Yuksekdag was detained in Ankara within the framework of a terror investigation, the state-run Anadolu news agency said.
Their detention appeared part of a large-scale operation against the HDP, which is the third largest party in the Turkish parliament.
Anadolu did not give further details on the investigation but NTV television said the pair were accused of spreading propaganda for the outlawed Kurdistan Workers Party (PKK).
It listed the names of half a dozen other HDP lawmakers who had been detained so far in the operation.
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Their detention followed a previous resolution by parliament allowing the immunity of MPs to be lifted.
The detentions come as Turkey remains under a state of emergency imposed in the wake of the July 15 failed coup, which critics say has gone well beyond targeting the actual coup plotters.
Tensions have surged in the Kurdish-dominated southeast of Turkey since a fragile ceasefire declared by the PKK collapsed in 2015.
The HDP seeks to promote the cause of Turkey's Kurdish minority and defend the rights of Kurds as well as those of women, gays and workers.
The charisma in particular of Demirtas -- dubbed the "Kurdish Obama" by some admirers after the US president -- earned it success at the ballot box.
It also divides all its top jobs between a man and a woman, as with the party chairmanship, which is shared between Demirtas and Yuksekdag.