Additional Chief Judicial Magistrate Priyajit Chatterjee remanded the two to police custody for 14 days after they were produced amidst tight security.
Munda, who carried out subversive activities in West Bengal, Jharkhand and Orissa and Murmu were wanted in connection with killings in Nayagram and encounters with the police.
While Munda was the squad leader of Nayagram-Gopiballavpur, Murmu was the squad leader of Jhargram.
Earlier reports had given Baneshwar Murmu's name as Jayanta.
They were arrested yesterday by the joint forces in a forested area near a pond at Chunghati village.
Jhargram superintendent of police Bharati Ghosh said the two used to often visit villages in search of food.
The arrest was based on information provided by an arrested member of Munda's squad.