That changed when they carried out synchronised bomb explosions in 63 of the country's 64 districts on Aug 17, 2005.
The government refused to accept their existence immediately, but had little choice when they surfaced in name of Jama’atul Mujahideen Bangladesh (JMB).
After four militant organisations, including JMB were banned and many of their leaders hanged, the law enforcing agencies got complacent, imagining they had wiped out militancy.
In 2013, the Islamist militants resurfaced with some vigour, attacking 'apostate bloggers' in the wake of the Shahbagh movement demanding maximum punishment for 1971 war criminals.
Since 2014, Bangladesh has witnessed targeted attacks on writers, online activists, publishers, Hindu and Christian priests, foreigners and members of Shia community.
Intelligence agencies believe Canadian-Bangladeshi Tamim Chowdhury is leading the 'Neo JMB'.
The Middle East-based Islamic State (IS) and al-Qaeda claimed responsibility for some of these murders.
The IS even reportedly uploaded pictures of the Jul 1 Gulshan cafe attack almost immediately after the mayhem and owned up the attack, in which 20 diners, including 17 foreigners, were butchered in cold blood.
But Bangladesh agencies blamed 'home-grown militants' for the attacks and the reported involvement of the JMB began to do the rounds again.
Eleven years after it first surfaced in 2004, the JMB is still believed to be a potent force.
Intelligence officials say that the JMB had split into several factions and one of it has re-surfaced as 'Neo-JMB'.
They say few other militant groups, all of the radical Islamist hues like Ansarullah Bangla Team, have merged with the 'Neo-JMB'.
Islamist militancy in Bangladesh started with the surfacing of Harkat-ul-Jihad-al Islami (HuJI), set up by some Bengali veterans of the anti-Soviet jihad in Afghanistan of the 1980s.
HuJI activists held processions in the capital Dhaka in the early 1990s.
In 1999, HuJI activists bombed the Udichi cultural event at Jessore.
In 2001, they bombed the Bengali New Year celebrations at Dhaka's Ramna and a rally of the Communist Party of Bangladesh at the capital’s Paltan.
HuJI was also blamed for the attack on a church in Gopalganj and the Awami League office at Narayanganj and finally for the murderous grenade attack on Sheikh Hasina-led Awami League rally at Dhaka’s Bangabandhu Avenue on Aug 21, 2004.
That the HuJI was behind the attack on writer Prof Humayun Azad outside the Book Fair premises and on Rajshahi University professor Md Yunus was not clear at that time.
But when the nation woke up to the serial explosions across Bangladesh on Aug 17, 2005, the JMB and not the HuJI was held responsible by intelligence agencies.
The 'Neo JMB' is being blamed for the Gulshan cafe attack, which left 22 people killed.
Intelligence officials say that though the JMB had surfaced in 2004, it was formed much earlier in the 1990s. They had also conducted drills before surfacing, the officials say.
After the Aug 17 series blasts, the JMB came to be associated with suicide attacks and killings like that of the judges at Jhalakathi and attacking the Gazipur Bar.
When JMB's chief Sayakh Abdur Rahman and its top terrorist Siddikul Islam alias Bangla Bhai were hanged over the murder of the Jhalakathi judges, there was a perceptible drop in JMB activity.
But after 2013, as a section of the JMB regrouped and gained strength by joining hands with other groups like Ansarullah Bangla Team, its tactics changed.
They now began to go for select assassinations.
Targets were carefully picked up—secular bloggers and writers, publishers and priests of minority communities, and especially foreigners were hacked to death ruthlessly.
In the process, the JMB gave up its preference for bombings and resorted to machetes and sharp weapons and small arms to carry out the assassinations.
The JMB may have been associated with madrasa educated boys mostly from rural poor background, but the 'Neo-JMB' is different.
Its new recruits are often drawn from upper middle class or rich families exposed to English-medium education and modern technology. That is what detectives are finding it so difficult to double-guess their moves or future plans.
The change in Bangladeshi Islamist militant tactics owes itself to changes in the global situation, says former Bangladesh Police chief Nurul Huda.
"Intelligence holds the key to taming the present phase of Islamist militancy. It is good that a counter-terrorism unit has been created," Huda told bdnews24.com
Alarm bells rang about a resurgent JMB after its activists manage to kill policemen and whisk away three JMB leaders from a prison van at Trishal in Mymensingh in 2014.
But it is only after the Jul 1, 2016 Gulshan cafe attack that intelligence agencies admitted the rise of a 'Neo-JMB' led by Tamim Chowdhury, a Canadian-Bangladeshi.
Former military official Shakhawat Hossain told bdnews24.com: "As far as I know, JMB is divided into three factions. One is the old JMB, whose leaders have mostly been hanged. This is no longer a very big faction. Police says a faction made up of newer recruits is much stronger"
Middle East based Islamic State has said Abu Ibrahim al Hanifa is the head of its Bangladesh chapter. Intelligence officials said this al Hanifa is none other than Tamim.
"I can’t say whether al Hanifa and Tamim Chowdhury are the same, but it appears that Tamim heads the JMB faction that has close links with the IS," Shakhawat Hossain told bdnews24.com.
He said that if Tamim is heading this new JMB faction, it is the one, which has regrouped and reorganised itself. "They have no link to the old JMB."
"This Tamim-led faction is primarily made up of the Internet generation. But it also has some madrasa students in its fold. It is quite remarkable how they have managed the two different social strands in their organisation.”
Hossain, a former brigadier, feels the third JMB faction could be the one that has merged with the Ansar al Islam or the Ansarullah Bangla Team.
"The Ansar al Islam was born out of the al Qaeda. Ansarullah Bangla is their cyber identity used for training.
“The Iraq based al Qaeda split into two—one became the Syria-based al Nusra Front, the other faction was led by al Jawahiri, most of whose followers went over to IS," said Hossain.
He said the IS declares provinces or 'belayets' like Egypt, Yemen and Libya whose heads maintain direct links with the IS headquarters.
"In all other areas, the IS gets local Islamist groups to work for them, like Katibah Nunsantara."
Hossain said groups like the 'Neo-JMB’ could well be working for the IS — and perhaps launching one attack after another to earn an IS affiliation after proving their credentials.
Dhaka University professor Delawar Hossain says the new group, responsible for these attacks, better be called 'Neo-JMB" rather than IS.
"IS owned up attacks on US mainland but US authorities insist the IS has nothing to do with those attacks. Even in France, Germany and UK, elements encouraged or inspired by the IS have launched attacks."
Hossain, who teaches international relations, said IS has tended to claim responsibility for attacks launched anywhere in the world. “This is to create an aura of terror about its persona."
Arguing all such attacks better not be ascribed to the IS, Hossain said that the IS trademark is random mass killings.
"But in Bangladesh, all these are targeted killings, designed to create a political situation. Killing Hindus to rattle India, Christians and foreigners to rattle the West, killing Japanese to rattle Bangladesh's biggest development partner," Delawar Hossain said.
Hossain said Islamist militancy in Bangladesh will not work.
"Look at our voting patterns, the biggest Islamist party gets only five percent of the votes. So, Islamist terrorism will find few takers in Bangladesh, if at all."
He argued that the homegrown Islamist militants may try for global affiliations like that of the IS, but ultimately their aims are to create 'short-term domestic political instability.’