The suspect, Shariful Islam alias Shihab, has been detained from Kushtia early today, said Dhaka metro police (DMP) spokesperson Deputy Commissioner Maruf Hossain Sardar.
Police said that the suspect belongs to an Islamist militant outfit.
"Shihab is an activist of the Ansarullah Bangla Team. They have been hiding in Khulna since the killing," Detective Branch Deputy Commissioner Mashrukur Rahman Khaled.
On the evening of Apr 25, assailants barged into the apartment of Xulhaz Mannan, a programme officer with the USAID and an editor of Bangladesh's first LGBT magazine.
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Xulhaz and his theatre activist friend Mahbub Rabbi Tonoy were hacked with meat cleavers on their head and neck, which forensic experts said was to ensure instant death.
Militant outfit 'Ansar Al Islam', which claims to be the Bangladesh affiliate of al-Qaeda, had claimed responsibility for the killings as well as six other previous killings of bloggers-online activists and the publisher.
Witnesses said five to seven people, clad in T-shirts and jeans, were involved in the killings and fled the scene after firing from guns, shouting 'Allahu Akbar'.
A patrol police officer was also injured while trying to stop them.
He, however, managed to snatch a bag from one of the assailants, inside which two firearms, ammunitions and a mobile phone were found.
Xulhaz's family filed a case over the murders the same day against five to six unidentified men while police initiated another over the attack on one of its men and the seizure of firearms.
There have been systematic assaults in Bangladesh in recent weeks especially targeting minorities, secular bloggers, intellectuals and foreigners.
In the latest attack, a 70-year-old Buddhist monk was hacked to death yesterday inside a remote monastery in Bangladesh, with police saying the incident bore the hallmark of previous killings of secular bloggers and minorities by Islamists.
On April 30, a Hindu tailor was also hacked to death by machete-wielding ISIS militants in his shop.
The ISIS and Al-Qaeda in Indian Peninsula have claimed responsibility for some of the attacks although the government denies their presence in Bangladesh.