They were arrested late in the night after crime branch officials questioned them.
Krishnankutty and Anarkali, in whose name the licence for the fireworks display had been taken, were picked up earlier in the day from Pallickal here, police said.
The two had been absconding since the devastating mishap during the festivities at Puttingal Devi temple on April 10, which claimed 108 lives and left over 300 injured.
The couple has moved an anticipatory bail petition in the Kerala High Court, saying they had been conducting the fireworks display for the past 40 years with proper licence that was valid till March, 2017.
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So far, 25 people, many of them workers employed by the contractors, have been arrested in connection with the incident.
Police have registered cases for offences, including attempt to murder against the accused.
Meanwhile crime branch officials probing the case today seized some files, hard disks and CCTV footage from the Kollam district collectorate tonight.