That, analysts said, could in turn complicate the timeline for the withdrawal from Afghanistan of remaining American troops, as they potentially come under new threats and see efforts to build a more stable political environment endangered.
The Taliban confirmed only on Thursday that Omar was dead. It is unclear who within the organization had been aware of his death, as well as which foreign governments.
While not seen as a commander of Taliban forces on the battleground, Mullah Omar was perceived as a supreme spiritual leader by various Taliban factions and set the overall direction for the group.
There have already been a small number of Taliban figures who have left the group on their own and since declared their fealty to ISIS, but the publicity of Omar's death may create the impetus for an even larger exodus without the "Commander of the Faithful," whose presence seemed to keep the groups more centralized and aligned on the larger issues confronting them.
"At the end of the day, the one person who could tie all these people was Mullah Omar," said CNN National Security Analyst Peter Bergen.
The Taliban's supreme council unanimously decided during a meeting in Afghanistan that Mullah Akhtar Mohammad Mansour will be the Taliban's new leader on Thursday, according to sources at Geo News, a CNN affiliate.
Mansour formerly headed the council, also known as the Quetta Shura, which is composed of longtime leaders who direct the Taliban's operations from Pakistan's Balochistan province, in addition to other positions within the organization. He was appointed Omar's deputy in 2010.
Omar was already overseeing the Taliban movement in Afghanistan before the 2001 invasion by the United States. He was also seen as the nominal leader of the Pakistani Taliban based in the tribal territories of northwest Pakistan. Other terrorist groups in the region like al Qaeda and the Haqqani organization pledged support to his leadership as well.
The geographical distribution of those various groups, coupled with the absence of an overarching focus of direction, may present a fertile environment for ISIS to exploit.
The fact that he has been dead for some time indicates that the organization can continue without him, however. though widespread awareness of his death might change how effective those at the top who have been operating without him can still be.
"With no Mullah Omar around, the various factions of the Taiban may just split up," Bergen said. "There will be more Taliban groups who might be inclined to swear their allegiance" to ISIS leader Abu Bakr al-Baghdadi, who has received pledges of allegiance from adherents from around the world.
And that creates potential complications for the United States as it continues transitioning to a new relationship with Afghanistan after more than a decade of war.
Difficulties for the U.S. in Afghanistan
For now, the U.S. policy is likely to remain the same: support the Afghan government with its security challenges; defend and extend the gains of the last 14 years; and try to get the Taliban invested in a peace-and-reconciliation process that allows them to become a part of the legitimate political process and, hopefully, dims its military activities.
But if more extreme factions develop -- or the Taliban as a whole is pulled in a more extreme direction -- that could jeopardize th effort.
Afghan President Ashraf Ghani has already endorsed the discussions underway to bring the Taliban into the effort to quell some of the violence that has plagued the region for decades
That scenario is likely to become more challenging if different Taliban factions with competing interests dominate the process, or if Mansour does not have the same unifying effect that Omar, who was said to have blessed the idea of the talks, had.
Pakistan's foreign ministry released a statement Thursday announcing that a second round of meetings between Taliban representatives and the Afghan government originally scheduled for this Friday had been postponed. The two sides kicked off negotiations earlier this month in Pakistan.
There is also the question of U.S. military involvement inside Afghanistan in support of the NATO mission that replaced the formal combat mission at the end of last year.
With nearly 10,000 American troops training Afghan security forces while also retaining the ability to mount counter-terror operations inside the country, a splintered Taliban movement that creates space for ISIS to grow could complicate plans to draw down American forces as planned.
At the urging of the Afghan government, Obama slowed down the transition earlier this year, but with a December 2016 deadline for the removal of all American troops from Afghanistan, a different and more dangerous security environment could open that up for further discussion.