The suspect’s name was not immediately announced but a statement gave his initials in Arabic variously transliterated as GA or JA.
Officials said the man had travelled to Syria to fight with Jabhat al-Nusra, before joining Isis, where he allegedly built relationships with field commanders including the "mastermind" behind the atrocites in Paris, and others threatening attacks in France and Belgium.
A spokesperson for Morocco's interior ministry said the man was arrested on Monday in Mohammedia, near Casablanca, after travelling through Turkey, Germany, the Netherlands and Belgium.
Several arrests have been made in relation to the Paris attacks in Morocco, where a warrant was also issued in November for fugitive Salah Abdeslam.
The 26-year-old French-Moroccan national was born in Brussels, where investigations have since traced him to a flat where suicide belts were manufactured.
He is thought to be the last member of the terror cell who murdered 130 people in the French capital at large, after fleeing to Belgium and then disappearing the following day.
The Moroccan warrant was issued as international manhunt continued, although there was no indication he was in the country at the time.
Abdeslam’s brother, Brahim Abdeslam, blew himself up on the Boulevard Voltaire, and he reportedly met alleged “mastermind” Abdelhamid Abaaoud in prison.
The Isis militant’s younger brother, Yassine Abaaoud, had been arrested in the Moroccan city of Agadir in October after landing in the country.
Moroccan authorities have arrested scores of suspected Isis militants in recent months, including a cell allegedly planning a bombing attack.
Around 1,500 Moroccan nationals are believed to be fighting with armed groups in Syria and Iraq.
Authorities estimated that around 220 have returned home and been jailed and 286 have been killed by the end of last year.
Additional reporting by Reuters and AP
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