Police recovered 197,000 US dollars, two firearms and clips from his apartment (in picture).
A 34-year-old Uzbek man confessed to carrying out the Istanbul nightclub attack on New Year's Eve, hours after he was captured in police raids.
Turkish police captured Abdulgadir Masharipov in raids conducted in Istanbul's western Esenyurt district.
Abdulgadir Masharipov still shot handed out by Turkish police from the video he took before he went on a shooting spree slaughtering 39. (AFP)
Masharipov was part of the Central Asian IS cell and was using the code name Ebu Muhammed Horasani.
Istanbul governor Vasip Sahin said "The terrorist confessed his crime," adding that Masharipov's fingerprints matched that of the attacker.
"He was trained in Afghanistan and can speak four languages. He's a well-trained terrorist," Sahin said.
At least 2,000 police personnel were involved in the operation.
They recovered 197,000 US dollars, two firearms and clips from his apartment.
The police had been tracking Masharipov for three days before detaining him to identify any associates.
The police also arrested an Iraqi man, three women, one an Egyptian and two from Africa.
The arrest of Masharipov could help discover other Islamic State cells in the country.
Police had released images during the manhunt, which were taken from the video Masharipov took just before embarking on the shooting spree.
The Reina nightclub attack was the first major attack in Turkey which the Islamic State claimed responsibility for.
"It is clear that the attack was carried out on behalf of Daesh (Arabic acronym of ISIS)," Sahin said.
During the investigation, police had initially suspected ethnic Uighur's from China to be involved in the attack.
Since the attack, the police has conducted 152 raids and detained 50 people.
President Recep Tayyip Erdogan congratulated the police and said "From now on in this country nobody will get away with what they have done."
"Everyone will be brought to account within the rule of law."
(WION with inputs from AFP)