In an interview with Syria’s Al-Baath newspaper published on Thursday, Assad said that the Brotherhood "takes advantage of religion and uses it as a mask... and it thinks that if you don't agree with it politically, that means you don't stand by God.”
But "this is not the case with Iran and Hezbollah," the Syrian president added.
Hezbollah "does not judge people based on religion or sect, but rather on patriotism and politics," said Assad.
Ever since mass protests led to the removal from office of Egypt's President Mohamed Morsi, Assad and his government have launched numerous attacks on the Muslim Brotherhood.
The Brotherhood's Syrian wing, persecuted for decades in Syria, is a key component of the so-called opposition National Coalition.
Assad also said that the country’s ruling party leaders removed in a reshuffle this week had made mistakes while in office.
The interview was published two days after the Baath party announced the names of 16 new leaders, which included none of the party's former chiefs with the exception of Assad, who will remain secretary general.
"When a leader does not solve a series of errors, this leader must be held accountable," Assad told Al-Baath newspaper, without elaborating.
"This is the real role of the (Baath party's) central committee, which is supposed to hold accountable the leaders on a regular basis. This did not happen in recent years," he added.
The central committee should "monitor the leadership's work, evaluate it and hold the leaders accountable", said Assad.
The reshuffle came more than two years into a foreign-backed deadly unrest that has left thousands dead in Syria.
"Those defending the nation now are the workers and farmers... some of them are in the army, others defending their land," said Assad.
"The struggle now is between those who are ignorant and those who are aware, between the patriots and the collaborators, between extremists and moderates."
The Baath party has been in power since March 8, 1963.
Until February 2012, the Syrian constitution described the Baath as the ruling party of Syrian society.
The constitution has been modified and a new article introduced enshrining the principles of pluralism and democracy. The party's reshuffle was the first since 2005.
Crisis in Syria started in March 2011, when pro-reform protests turned into a massive insurgency following the intervention of Western and regional states.
The unrest, which took in terrorist groups from across Europe, the Middle East and North Africa, has transpired as one of the bloodiest conflicts in recent history.
As the foreign-backed insurgency in Syria continues without an end in sight, the US government boosts its political and military support to Takfiri extremists.
Washington has remained indifferent about warnings by Russia and other world powers about the consequences of arming militant groups.
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