As the security situation in Afghanistan deteriorates and the Taliban seem incapable of defeating Islamic State-Khorasan Province (ISKP) and protecting religious minorities, Tehran is alarmed about the potential outbreak of a civil war next door and the chances that such a conflict might spill over into Iran. Under these circumstances, Iran may look for more effective means of countering ISKP.

There are conflicting reports about Iran's engagement with al-Qaeda and other Sunni extremist groups. Some even claim Iran has become al-Qaeda’s principal operating base. While this seems dubious, Iran has a long history of using one enemy against another.

In 2015, when Tehran concluded that the previous Afghan government could not combat ISKP militants, Iran expanded its active engagement with the Taliban. With rising security concerns along Iran's eastern border, Tehran may try to take advantage of the rivalries among extremist groups. However, Iranian leaders might be missing a more effective weapon to fight ISKP and similar groups: winning the hearts and minds of Iran’s own Sunni population.

The (exaggerated) links between Iran and al-Qaeda

Some U.S. officials, including former U.S. Secretary of State Mike Pompeo, have repeatedly called Iran a new stronghold for al-Qaeda. Al-Qaeda "is operating under the hard shell of the Iranian regime's protection," Pompeo said in 2021, labeling Iran as "a new Afghanistan" in reference to the period from the 1990s until 2001 when Afghanistan hosted al-Qaeda leaders. Iran denied this accusation, and Pompeo's claims do not seem to be consistent with the judgment of the intelligence community at the time that the relationship between Iran and al-Qaeda "is not one of terrorist collaboration.”

Iran and al-Qaeda-like groups do not have compatible ideologies. Shi’a Iran and Sunni Wahhabi/Salafi organizations like al-Qaeda are implicitly at odds with one another. Supreme Leader Ayatollah Ali Khamenei once even blamed the United Kingdom, United States, Israel, and the Sunni Gulf states for supporting such groups in order to fight Iran and Shi'ism. "But these are not the main enemies, and the main enemy is the one who provokes them and gives them money," Khamenei said in 2013.

Nor has there been much evidence connecting Iran with the Sept. 11, 2001 attacks, as some claimed. Iran cooperated and provided essential assistance to the United States and coalition forces regarding al-Qaeda and the Taliban. Relations between Iran and the United States soured when Iran, despite genuine cooperation with the United States, was branded, along with Iraq and North Korea, as part of the “Axis of Evil” by then-President George W. Bush.

Many al-Qaeda members and their families fled to Iran after the fall of the Taliban in 2001. Some were imprisoned and the Iranian government denied there were any al-Qaeda members in Iran for many years. In 2013, when Canadian police discovered a terrorist plot and two suspects were charged with having received support from al-Qaeda inside Iran, Iran's then foreign minister, Ali Akbar Salehi, called it "the most laughable claim ever.”

Iran’s use of extremist groups

There is no evidence of direct Iranian government support for Salafi groups. Kurdish activists, however, suspect that these groups were tolerated by the authorities in Tehran. Kurdish activists claim that the government has promoted Salafist Wahhabi thinking in the past to prevent the expansion of Kurdish nationalist or leftist groups and NGOs. The Salafis reject any activities promoting civil society and they have generally fought all NGOs. They are also at odds with any organization or entity that promotes statehood, potentially making them an effective tool to combat Kurdish separatists and nationalists.

In the past, especially when there was a heightened threat perception of American military attacks across Iran’s eastern or western borders, the government’s support for Salafists seemed to be aimed at letting them fight the U.S. due to their strong anti-American sentiment. What else would explain the extremely harsh treatment of Kurdish leftist and separatist prisoners compared to Salafist Wahhabi ones, Kurdish activists ask?

The issue of the Salafi presence in Iran was discussed more broadly after two simultaneous terrorist attacks occurred in Tehran on June 8, 2017, against the Iranian Parliament building and the Mausoleum of the Founder of the Islamic Republic, Ayatollah Ruhollah Khomeini. The attacks, which killed 17 civilians, were carried out by ISIS.

Afghanistan: Iran's Achilles’ heel 

Concerns about the insecurity of its eastern borders have become Iran's number one priority, especially since the Taliban's takeover of Kabul in August 2021.

In early 2015, Tehran consciously worked to improve its relationship with the Taliban after it became convinced that the then-Afghan government was not strong enough to defeat ISKP. While portraying their engagement with the Taliban as an attempt to facilitate intra-Afghan dialogue — that is to say, negotiations between the Taliban and the Afghan government — Iranian leaders also tried to increase their influence within the group. Although Iran has had some success, it will not be able to compete with traditional Taliban supporters, such as Pakistan, Saudi Arabia, the UAE, or even Turkey and Qatar.

Iran may have some friends within the Taliban, but it is in the dark about the group's structure and has little influence over its leaders, many of whom have ties to Iran's regional rivals. The Taliban’s takeover of Afghanistan has been, perhaps, one of Iran's most critical recent security challenges. Iran has been concerned about the return of a regime to power that has refused to be inclusive in any way. Iranian leaders worry about the Taliban’s treatment of religious and ethnic minorities and their inaction in protecting these communities. Reports indicate that since the Taliban came to power in August 2021, at least 13 attacks against Hazaras by the ISKP have left many dead and hundreds injured. The April 21 suicide bombing at Seh Dokan Mosque in Mazar-e Sharif, one of the country’s most prominent Shi’a mosques, which left 31 dead and 87 wounded, is but one such example. Tehran is also concerned over the Taliban’s disinterest in its security priorities, including border security, smuggling, and refugees.

Iranian officials have had to explain to the public why they’ve adopted such a friendly tone toward a regime with which they nearly went to war two decades ago. Hardline Iranian media has painted a friendly picture of the Taliban. "The Taliban forces we know today are different from the Taliban we knew in the past and the Taliban that would conduct beheadings of the people," the hardline Kayhan newspaper wrote in an editorial on June 21, 2021. There was an outcry in Iran calling on the government to support Ahmad Massoud, the leader of the National Resistance Front of Afghanistan and son of the late Northern Alliance leader Ahmad Shah Massoud.

The confusion over Iran's official position toward the new Taliban regime was so intense that Gen. Esmail Qaani, commander of the Islamic Revolutionary Guard Corps (IRGC) Quds Force, held a closed-door meeting with parliament members on Sept. 7, 2021. He explained the IRGC's policies in Afghanistan and brushed aside speculation that Iran was confused over how to deal with the Taliban. Iran "has a good grasp on Afghanistan's issues … and it is not as if the Islamic Republic of Iran has been surprised by the events," Qaani told the MPs.

Concerns about terrorist infiltration

Iran's official position toward the new Afghan regime was highly cautious, meant not to irritate the new rulers and, at the same time, to prevent a flood of refugees into the country. Hundreds of Afghan army personnel who fled to Iran upon the Taliban's takeover were deported back, for example. However, Iran could not prevent that flood of refugees, who came not just from neighboring provinces with cultural and linguistic ties, such as Herat, but from all parts of Afghanistan. The number was so great that authorities had to hire Pashtun translators to communicate with the refugees.

Unregistered Afghan refugees have been one of Iran's most significant challenges since the Taliban takeover. There are no migrant camps in Iran like those in other countries, such as the Syrian camps in Turkey. Harsh treatment of migrants and a complicated registration process frequently encourage refugees to skip registration with the goal of passing through Iran to a third country. Consequently, many people may have entered Iran without proper records or any sort of monitoring. Iranian authorities are concerned that this group could include potential terrorists. There have been incidents, such as a knife attack on three Iranian clerics in Mashhad back in May, which was described as a “terrorist attack committed by Takfiri and Salafi” sympathizers.

Iran's challenges in dealing with the Taliban

Iran’s primary challenge in dealing with the new Taliban-led Afghan government seems to lie in the realm of border security. Clashes along the Iran-Afghanistan border have grown more frequent since the Taliban takeover, including recent skirmishes in the border region of Nimroz Province in Afghanistan and Hirmand in Iran. One of the clashes was so profound that residents of the region left their homes out of fear of escalating violence. Each country blamed the other for the episode. Iranian officials have been conciliatory about these incidents, arguing that the Taliban is "new to the border-related regulations" and "unfamiliar with the international principles and laws." Similarly, the Taliban have called the border incidents "misunderstandings."

There is concern that the Taliban could misinterpret too much Iranian patience as weakness. Some, including Mohsen Roohi-Sefat, former foreign minister deputy chief for political and international studies, warn that "anti-Iran countries" could use their influence within the Taliban to harm Iran. 


Border security appears to be Iran’s greatest point of weakness when it comes to Afghanistan. The threat of ISKP or similar groups has made Iran more vulnerable than ever, and this concern could drive Iran to seek new alliances. The bitter lesson Tehran should draw from its previous attempts to use one extremist group against another is that this tactic has never produced a positive outcome. History, including that of the Islamic State, which emerged out of the remnants of al-Qaeda in Iraq, has shown that these groups often evolve and become more dangerous over time.

The Iranian government has put all its efforts into defeating militant Sunni groups using military means, neglecting the important task of winning the hearts and minds of Iran’s Sunni population. Tehran’s discrimination toward and harsh treatment of Iranian religious minorities has proven counterproductive. These policies have alienated those populations and, in the process, created a breeding ground for violent extremism. The Islamic Republic might be more successful in its fight against extremist Sunni groups if it tried to win the trust of Iranian Sunnis and provide them with fundamental religious freedom.


Fatemeh Aman is a non-resident senior fellow at the Middle East Institute. She has written on Iranian, Afghan, and broader Middle Eastern affairs for over 20 years. 

Photo by Sayed Khodaiberdi Sadat/Anadolu Agency via Getty Images

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