There's a growing fear in the North African country where the pro-democracy uprisings of the so-called Arab Spring were triggered in January 2011 that the militants will return and take over the revolution from moderate parties.
That would turn Tunisia into another battleground for al-Qaida and its allies, who are locked in conflict with French forces, backed by African troops, in northern Mali. Al-Qaida in the Islamic Maghreb established a stronghold in the region in early 2012.
French-led forces have driven militants into the mountains but regional and Western intelligence services are concerned that al-Qaida is building new power bases in places such as Syria, Yemen and Tunisia.
Right now, the growing dominance of jihadist groups among rebels fighting the Syrian regime of President Bashar Assad means the militants' focus is at the other end of the Mediterranean.
But on March 27 the leader of Tunisia's jihadist movement Ansar al-Sharia, Saifallah bin Hassine, threatened to topple the country's Islamist-led government under Prime Minister Ali Larayedh.
The threat, the most direct against the moderate Ennahda government by the Tunisian jihadists and published on Ansar al-Sharia's Facebook page, said, "Keep your diseased persons on from us or else we will wage a war against him until their downfall and they are thrown in the dustbin of history."
U.S. and Tunisian authorities are increasingly worried. Larayedh has spoken of "an inevitable confrontation."
Last week, U.S. Army Gen. Carter Ham, head of the U.S. Africa Command, declared, "It's very clear to me that al Qaida intends to establish a presence in Tunisia."
The threat came the day after Larayedh accused bin Hassine, wanted for masterminding an attack on the U.S. Embassy in Tunis Sept. 14, of inciting violence and arming his followers as more moderate political forces seek to conduct the delicate transition from the dictatorship of longtime ruler Zine el-Abidine Ben Ali, who fled in January 2011.
His followers were allegedly behind the Feb. 6 assassination of popular secular politician Chokri Belaid, triggering a political crisis that led to Larayedh taking over from Prime Minister Hamadi Jebali.
Security authorities have uncovered several large arms caches in recent weeks and rounded up scores of suspected militants.
Arab intelligence sources say the Tunisian jihadists are running major networks smuggling in arms, as well as aiding al-Qaida affiliates in Mali and elsewhere in North Africa.
In December, there was a major shootout on the Algerian border when a large cache of arms and ammunition was seized.
But as one official lamented: "The security forces can't secure every border. The state can't be everywhere at the same time."
Many of the weapons are believed to have originated in Libya, which has been awash with arms since its 2011 civil war that toppled longtime dictator Moammar Gadhafi.
Libyan weapons played a major role in the takeover of northern Mali in 2012 by AQIM and its allies.
Many in Tunisia fear the arms inside the country are being stockpiled for use against the government if it continues to resist Ansar al-Sharia's demands for Islamist rule.
Observers say militant Islamists, banned under Ben Ali, have exploited the weakened security brought about by the revolution and the uncertainty, turbulence and the lack of economic development that ensued to widen their support base.
Statistics about jihadist strength are difficult to come by but President Moncef Marzouki estimated in October that there are around 3,000 militants.
Tunisia, a former French colony that secured independence in 1956, is a relatively small nation of around 10 million people but its militants have a history of supporting pan-Arab movements. They have fought in significant numbers in Afghanistan, Iraq, Syria and Mali.
Two Tunisian jihadists assassinated pro-U.S. Afghan warlord Ahmad Shah Massoud in a suicide attack at his mountain redoubt two days before the Sept. 11, 2001, attacks to eliminate a key anti-Taliban leader who could have rallied fighters against Osama bin Laden.
Tunisians constituted the largest national group among the 40 AQIM fighters who stormed the In Amenas gas complex in southern Algeria in January in which most of the 40 attackers and 39 foreign captives were killed.