"Lebanese authorities arrested Ahmad al-Assir this morning at the airport. He had changed his appearance and was trying to leave the country," a security source told AFP.
Security sources added that Assir was using a fake passport and was trying to fly to Egypt.
The firebrand cleric had been on the run since June 2013, after he and his supporters engaged in a deadly two-day battle with the Lebanese army in the southern city of Sidon.
He continued to issue audio statements while on the run, and various rumours circulated as to where in Lebanon he was hiding.
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In 2014, a military judge recommended prosecutors seek death sentences for Assir and 53 others, including singer-turned-fundamentalist Fadel Shaker.
He and his associates were accused of "having formed armed groups that attacked an institution of the state, the army, killed officers and soldiers, took explosive materials and light and heavy weapons and used them against the army."
He began making headlines after the conflict erupted by criticising Lebanon's powerful Hezbollah movement and its ally Syrian President Bashar al-Assad.
Although he was born to a Shiite Muslim mother, his discourse was highly sectarian and he often accused Lebanon's army of failing to protect Sunnis and being beholden to Hezbollah.
He encouraged his supporters to join Syria's mainly Sunni rebels and to rise up against Hezbollah.