A spokesman of the JKLF said Malik was arrested from his residence in Maisuma area. Other separatists are also likely to be arrested or put under house arrest.
Yasin Malik had on Friday given a slip to the police and had reached Charar-e-Sharif where he addressed a big congregation.
Malik along with Hurriyat leaders Syed Ali Geelani and Mirwaiz Umer Farooq has been spearheading the separatist resistance in the Kashmir Valley for over one year.
Reacting to the arrest, BJP MLA Ravinder Raina demanded that all other hurriyat conference leaders including Mirwaiz Umar Farooq, Shabir shah and others be immediately arrested under murder cases.