The kingdom has also designated al-Qaeda off-shoots Nusra Front and the Islamic State in Iraq and the Levant, whose fighters are battling Syrian President Bashar Assad, as terrorist organizations. The list included the Saudi branch of Hezbollah, as well as Yemen's Shiite Hawthis.
The Interior Ministry statement said King Abdullah approved the findings of a committee entrusted with identifying extremist groups referred to in a royal decree earlier last month.
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Friday's move appeared to enforce last month's royal decree where Riyadh said it would jail for between three and 20 years any citizen who fought guilty of fighting in conflicts abroad.
The kingdom's authorities want to deter Saudis from joining rebels in Syria and posing a security risk once they return home.
Riyadh also fears the Brotherhood, whose conservative Sunni doctrines challenge the Saudi principle of dynastic rule, has tried to build support inside the kingdom since the Arab Spring popular revolutions in the Arab-speaking world.
In Egypt, the Brotherhood, which won every election following the toppling of long-time ruler Hosni Mubarak in 2011, has been driven underground since the army deposed President Mohamed Morsi, a longtime member of the group that also endured repression in the Mubarak era.
Saudi Arabia's Islamic religious authorities have previously spoken out against Saudi fighters going to Syria, but the Saudi Interior Ministry estimates that around 1,200 Saudis have joined the fighting there nonetheless.
The Associated Press and Roi Kais contributed to this report