The victim, Irshad, was missing since July 18. He was reportedly in a relationship with the sister of the accused, SSP Deepak Kumar said.
The victim's body was recovered from the house of the accused in the district yesterday, he said.
The accused, Pawan Kumar and Pintu, have been arrested in this connection, police said.
The incident had sparked protests with many blocking the Khatima-Panipat highway at Jansath area last night. Jansath SHO, Ajaypal Gautam was also transferred in the case.