KISMAYO, Somalia — Some say the Americans are everywhere. Some say they are nowhere. Still others say they are everywhere and nowhere at once. But the shadowy U.S. presence in this strategic port city in war-torn southern Somalia has clear consequences for anyone with a share of power here. That includes Somali regional officials who are quick to praise American counterterrorism efforts, African Union forces who rely on U.S. intelligence as they battle back al-Shabab, and even the al Qaeda-linked militants themselves, who are increasingly hemmed in by a lethal combination of AU-led counterinsurgency, airstrikes, and raids by U.S. special operators.

Based out of a fortress of fading green Hesco barriers at the ramshackle airport in Kismayo, a team of special operators from the Joint Special Operations Command, the elite U.S. military organization famous for killing Osama bin Laden, flies drones and carries out other counterterrorism activities, multiple Somali government and African Union sources have confirmed. Their presence in this volatile city, which until 2012 was controlled by al-Shabab, has not previously been reported. Nor has the United States acknowledged operating drones from Somali soil. (Unmanned armed and surveillance flights are said to originate from Camp Lemonnier in nearby Djibouti or from bases in neighboring Kenya and Ethiopia.)

“They have a base over there,” Abdighani Abdi Jama, state minister for the presidency in the interim regional administration in Kismayo, said of U.S. forces, gesturing to a heavily fortified compound not far from the airport’s small terminal. He confirmed that as many as 40 U.S. military personnel are currently stationed in Kismayo, roughly 300 miles south of the capital of Mogadishu, where he said they operate drones from the airport’s single runway and carry out covert “intelligence” and “counterterrorism” operations.

“They have high tech; they have drones; they have so many things,” said Jama. “We are really benefiting.” Another regional official, Jubaland’s minister of planning, international cooperation, and humanitarian affairs, Mohamed Nur Iftin, also confirmed the existence of the U.S. outpost and the use of the runway for drones, as did a cabinet-level official in Mogadishu. Kenyan Brig. Gen. Daniel Bartonjo, the sector-level commander for the African Union Mission in Somalia (AMISOM), the multinational peace enforcement mission that has been battling al-Shabab since 2007, said that his troops have made gains against insurgents “with the help of the Americans who are here.” He made this comment in a June 19 briefing in Kismayo for Nicholas Kay, the special representative of the U.N. secretary-general for Somalia, attended by this reporter.

The secretive outpost in Kismayo is one of several locations within Somalia where U.S. special operations forces have set up shop beyond the prying eyes of the Somali public — and the American public that foots the bill. Somali government and AMISOM sources confirmed the existence of a second clandestine American cell in Baledogle, the site of an abandoned Cold War-era Air Force base in Somalia’s sun-blasted Lower Shabelle region. These sources estimated that between 30 and 40 U.S. personnel are stationed there, also carrying out counterterrorism operations that include operating drones.

A spokesman for the U.S. Special Operations Command, which handles public affairs for JSOC, referred Foreign Policy to the U.S. Africa Command (AFRICOM) for comment. AFRICOM spokesman Chuck Prichard, in turn, confirmed that a “small number” of U.S. personnel within AFRICOM’s area of responsibility are special operations forces, but declined to comment on the size or location of their units. He also declined to comment on whether or not they are responsible for operating drones, saying only that they “are not tasked with directly engaging enemy forces.”

“While we cannot provide exact details because of operational security issues, we can tell you [U.S. AFRICOM] has sent a limited number of trainers and advisors plus a small military coordination cell to support AMISOM and Somali security forces in international efforts to stabilize Somali,” Prichard wrote in an email to Foreign Policy. “The sharing of information and expertise is key to assisting partner nations in their mission. The exact nature of this support, weapons systems or number of personnel involved in these operations cannot be disclosed in order to protect the integrity of these operations and the safety of units in the region.”

The expanded U.S. footprint in Somalia is part of a broader trend toward deeper covert military engagement in the volatile Horn of Africa region. That engagement has taken the form of ramped-up intelligence and special operations activities, as well as military assistance programs that have grown dramatically in recent years without much in the way of public debate or congressional oversight. As the U.S. Defense Department draws down its presence in Afghanistan and shutters bases across Europe, and as the threat of terrorism surges in East Africa, the quiet accumulation of military installations in this part of the world has been easy to miss. In addition to its main hub in Djibouti, where some 4,000 American service members and civilians are stationed, the U.S. military has established smaller outposts in Ethiopia, Kenya, and the Seychelles, a tropical archipelago located roughly 800 miles off the Somali coast. It has also indirectly financed the training of thousands of AMISOM troops.

U.S. boots on the ground

Even as it became firmly entrenched in the region, the U.S. government for years denied putting boots on the ground in Somalia, where the infamous “Black Hawk Down” disaster in 1993 sparked an American exodus from the region. But in June of last year, Undersecretary of State for Political Affairs Wendy Sherman acknowledged that a “small contingent of U.S. military personnel” had been operating inside Somalia for “several years.” The news agency Reuters later quoted an unnamed official of President Barack Obama’s administration as saying that there were “up to” 120 U.S. personnel stationed inside the country.

Although much of what the U.S. military does in Somalia remains shrouded in secrecy, it is clear that the Americans are doing more than just gathering intelligence and supporting African troops. In recent years, special operations commandos have staged a number of daring raids on al-Shabab targets, including an aborted amphibious assault in 2013 by Navy SEAL Team 6 aimed at capturing one of the suspects in the Westgate Mall attack, which took place in neighboring Kenya and left 67 people dead. U.S. forces have also carried out drone strikes and other airstrikes in Somalia since at least 2007, when an American AC-130 gunship fired the opening salvo in the Somali theater of the war on terror. That operation targeted a convoy carrying Aden Hashi Ayro, an al Qaeda operative thought to be responsible for the murder of Western aid workers. Ayro survived, only to be taken out by a U.S. missile strike one year later.

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