Islamic outfit PFI's Assam unit chief Aminul Haque was arrested on Wednesday along with another office bearer for their alleged role in the violence during protests over the citizenship law, police said.
Haque was arrested from his residence in Hatigaon area of the city, and a desktop computer, two laptops, documents and cane sticks were seized, they said.
Mujamil Haque, who is the Popular Front of India's Baksa district press secretary, was also arrested, they added.
Police, however, declined to share the details of cases registered against them and where they were registered.
Finance and Health Minister Himanta Biswa Sarma on Tuesday alleged that there may be a "deadly nexus" among a section of Congress workers, "urban Naxals" and PFI that tried burn down the state secretariat during the December 11 protests.
"You will clearly see that slowly a pattern of violence is evolving where the PFI and the CFI (Campus Front of India), which are offshoots of the SIMI, were behind the violence in Guwahati. They had a plan to demolish the city," he had said at a press conference.
Police said 215 cases related to violence during the protests have been registered, 329 arrests have so far been made and 2,026 persons detained.