Detective Branch (DB) of Dhaka Metropolitan Police arrested Allama Junaid Al Habib, central joint secretary general of Hefazat-e-Islam from the city on Saturday.
Habib, who was also the president of the Dhaka City unit of the radical organisation, was picked up from Baridhara area in the city.
DB Joint Commissioner Mahbub Alam confirmed the matter to the media.
Apart from the case filed against him on May 5, 2013 at Shapla Chattar, there are several cases against him at present, police sources said.
Earlier DB arrested another leader of Hefajat-e-Islam from Dhaka's Mohammadpur area.
Deputy Commissioner (DB) of Motijheel Division Police confirmed it.
He was identified as Maulana Jalaluddin Ahmed, an assistant secretary general of the Islamist group. A team of detectives detained him in Mohammadpur area.
Half a dozen of Hefajat leaders were arrested in last couple of days in connection with cases filed following the mayhem in 2013 and in the late march this year.
Meanwhile, Vice-president of Hefajat-e-Islam's Dhaka city unit Maulana Jubair Ahmed was placed on a five-day remand on Saturday in a case filed with Paltan Police Station over the 2013 mayhem in Dhaka.
Metropolitan Magistrate Mohammad Jashim passed the order.
Earlier, Md Kamrul Islam Talukder, an inspector of the Detective Branch of police, and also the Investigation Officer of the case, produced him before the court with a 10-day remand prayer in the case.
In the remand prayer, the IO said Maulana Jubair and other accused were directly involved with the incident on May 5 of 2013 in the city's Paltan area.
Howover, he refused to disclose the names of others who were responsible for the incidents and that is why he needs to be remanded to gather information about whereabouts of other accused, the IO added.
On the other hand, the defence submitted a petition seeking cancellation of the remand prayer saying that their client was implicated in the case as part of a conspiracy to harass him. Moreover, he was not present at the place of the mayhem, defence added.
Upon hearing both sides, the magistrate turned down the defence plea and placed Jubair on a five-day remand for quizzing.
Police arrested Jubair from his Lalbagh residence in the capital on Friday.
Jubair was also involved in the recent incidents of Hefajat mayhem during the Indian Prime Minister Narendra Modi's visit to Bangladesh and the subsequent hartal called by Hefajat on March 28 this year.
On May 5 in 2013, thousands of members of Hefajat, a Qawmi madrasa-based Islamist organisation, locked into a clash with law enforcers and ruling Awami League men, turning Motijheel and Paltan areas into battlefields.
A total of 83 cases were filed in seven districts, including Dhaka, accusing 3,416 named and 84,796 unnamed people.
Police have pressed charges in 18 cases and submitted final reports in two other cases. Investigations of 62 other cases have been stalled.