Yasin Malik was taken into custody from his Maisuma residence in Srinagar this morning, a police official said.
He said Yasin Malik has been lodged in police station Kothibagh.
The official said Mirwaiz Farooq was placed under house arrest at his Nigeen residence.
The separatists, under the banner of Joint Resistance Leadership (JRL), on Tuesday called for a protest strike for today against the killing of civilians allegedly in security forces firing recently and the killing of veteran journalist Shujaat Bukhari.
Shujaat Bukhari was shot dead, along with his two personal guards, outside his office in Press Enclave here on 14 June by unknown gunmen.