Superintendent of Police Rural, Alok Piryadarshi said Gaurav and Abhinao, who were absconding, were arrested from Moradabad.
The Special Investigation Team (SIT) probing the riots had found the involvement of 25 people in six gang-rape cases out of which 24 accused have been arrested.
Only one accused Amardeep, who is absconding, remains to be arrested in connection with gangrape cases during the riots, the SP said.
More than 60 people were killed and 40,000 displaced during riots in Muzaffarnagar district and its adjoining areas last September.