There was little surprise to see the Muslim Brotherhood topping the list, given the Gulf state's relentless efforts against the regional Islamist group.
But the inclusion of organisations such as the Washington-based Council on American-Islamic Relations (CAIR), Islamic Relief UK and some of the largest Muslim associations in Finland, Norway, Sweden and other European countries prompted outrage and calls from several Western governments for an explanation.
By casting its net so far and so wide, experts say, the UAE is pushing its view that the fight against militant Islamism is as much an ideological war as a conventional one.
The real target of the list, said Frederic Wehrey, a Gulf expert at the US-based Carnegie Endowment for International Peace, is "politically active Islamism".
"(The UAE) is trying to include non-violent, Brotherhood-affiliated groups in the same ideological constellation as real terrorist groups like (Nigeria's) Boko Haram and Al-Qaeda," he said.
The wealthy Gulf state, which boasts an open society that brings together millions of foreigners of 200 nationalities, at first seems an odd choice to lead the charge against political Islam.
Longer blacklist than US
The UAE has never been targeted by attacks and has not seen the kind of populist protests that have shaken other countries in the region.
The country's vastly rich leaders see a real threat to their rule however from the Muslim Brotherhood, a grassroots Islamist group that was formed in Egypt in 1928 and has expanded across the region.
"(The UAE) is trying to include non-violent, Brotherhood-affiliated groups"
"I think the criteria (for the list) has been to look at anything that could have even a remote link to the Muslim Brotherhood," said Andrew Hammond, a senior policy fellow at the European Council on Foreign Relations' Middle East and North Africa programme.
The UAE has pushed hard against the Brotherhood in recent years, jailing dozens of members, putting pressure on fellow Gulf state Qatar to end its support for the group and backing Egypt's anti-Islamist president, Abdel Fattah al-Sisi.
It has also used its increasing military power against Islamist insurgencies, bombing militant positions in Libya and joining the US-led coalition carrying out air strikes against Islamic State jihadists in Syria and Iraq.
Mustafa Alani, a security expert from the Geneva-based Gulf Research Centre, said the UAE may not be facing any "imminent or potential threat", but is increasingly worried by "the situation across the region and security developments in Syria and Iraq".
The UAE blacklist was released on November 15 and included 83 groups, far outnumbering Saudi Arabia's list of nine and even the US list of 59 designated "Foreign Terrorist Organisations".
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There were several interesting omissions, including Lebanon's powerful Iran-backed Hezbollah militant group and the Palestinian Hamas movement running Gaza.
But it was the inclusions that sparked debate.
CAIR, the most prominent Muslim civil liberties group in the United States, described its listing as "shocking and bizarre", pointing to its "many anti-terror initiatives".
"Like the rest of the mainstream institutions representing the American Muslim community, CAIR's advocacy model is the antithesis of the narrative of violent extremists," it said in a statement.
Islamic Relief in Britain expressed similar surprise, saying it assumed its inclusion on the list "can only be attributable to a mistake".
"We abhor terrorism in all its forms," the group said, noting its work with the International Federation of Red Cross and Red Crescent Societies, British authorities and the United Nations.
UAE officials have said groups can appeal through the courts to have their names removed from the list.
"This is available to organisations whose approach has changed," the minister of state for foreign affairs, Anwar Gargash, said on Twitter.
In a recent interview with US broadcaster Fox News, UAE Foreign Minister Sheikh Abdullah bin Zayed al-Nahayan suggested that those on the list were secretly backing and funding violent groups.
"We cannot accept incitement or funding when we look at some of these organisations," he said.
"For many countries, the definition of terror is that you have to carry a weapon and terrorise people. For us, it's far beyond that; we cannot tolerate even the smallest, tiniest amount of terrorism."
But Wehrey warned the UAE list could do more harm than good by "driving Islamist political movements underground".
"The UAE had long been insulated from terrorism," he said, "but its clear partisanship and excessive alarmism could prove to be a self-fulfilling prophecy."