National Democratic Front of the Philippines (NDFP) Consultant Rafael Baylosis is now under detention at the Philippine National Police (PNP) headquarters in Camp Crame, Quezon City.
This comes following his arrest yesterday along Katipunan Avenue and Aurora Boulevard in Quezon City.
His companion, identified as Guillermo Roque, was also nabbed.
The operation was conducted by the police and the Armed Forces of the Philippines (AFP).
Baylosis is the first rebel leader to be caught by the authorities after President Rodrigo Duterte ordered last November the arrest of all NDFP consultants who participated in the peace talks between government and the communist insurgents.
Baylosis is tagged as the "acting secretary" of the New People's Army (NPA) while Guerrero is reportedly an NPA member.
The arresting team said two .45 calibers were seized from Baylosis and Guerrero.
Charges of illegal possession of firearms are being prepared against them.
Aside from this, Baylosis is facing multiple murder charges following the discovery of a mass grave of alleged NPA victims in Leyte.