South Sudan’s Jonglei: Who burned homes and silenced hospitals?

Published 16 June 2026 · health

Juba, South Sudan – In the days before Lankien was attacked, doctors at the local hospital rushed to evacuate patients. Some were women in labour

Juba, South Sudan – In the days before Lankien was attacked, doctors at the local hospital rushed to evacuate patients. Some were women in labour. Others were being treated for gunshot wounds. By the evening of February 3, just hours after the last patients were carried out, a bomb struck the empty facility, ripping a crater through its warehouse. Fighting was underway in surrounding areas as South Sudan’s military pressed forward with a counteroffensive aimed at retaking territory seized by opposition armed groups. As the army advanced eastward through Jonglei State, it captured town after town, pushing opposition fighters towards the Ethiopian border. In the aftermath of the bombing, residents said they were forced to flee into surrounding marshland on the morning of February 7 as mortar fire struck the town. Some eventually returned and described extensive destruction. The hospital had been looted and burned. Its cold-chain storage unit, used to preserve vaccines, was set on fire. Vehicles were sprayed with bullets and stripped for parts. Solar-powered water systems had been dismantled. The local market was reduced to twisted metal sheets, while homes on the outskirts appeared to have been burned. “Anything that can support the life of human beings was deliberately destroyed,” said Emmerson Gono, deputy head of mission for Doctors Without Borders, known by its French initials MSF, who visited Lankien in April, adding that this was his assessment based on what he observed. A counteroffensive across Jonglei Since the start of what authorities refer to as “Operation Enduring Peace,” satellite imagery analysed by the Centre for Information Resilience (CIR), combined with verified videos, images and witness accounts, indicates widespread destruction across a swathe of Jonglei that has long been a stronghold of opposition groups. Both the military and opposition forces have been accused of razing villages and attacking civilians in recent months. In this area of Jonglei, which is home to a section of the Nuer ethnic group that officials often cast as hostile to the state, more than a dozen residents who spoke to Al Jazeera said they believed the military was responsible for targeted destruction that experts say has pushed tens of thousands of people towards the brink of famine. In most of the 23 incidents CIR documented between late January and February, civilian structures, including homes, health facilities and markets, appear to have been burned and looted.

CIR said the destruction was “likely to be more widespread and potentially part of what it described as a deliberate military strategy”. “Using satellite imagery, we were able to map how troop movements from west to east followed a path of burning and looting,” said CIR researcher Kiria Borak, stressing that satellite imagery alone cannot determine intent or responsibility. Some officials and humanitarian actors have attributed the destruction in Jonglei to clashes between government troops and opposition forces. However, residents told Al Jazeera that opposition fighters were not present when their villages were attacked. Those accounts could not be independently verified due to restricted access to the area. Government officials did not respond to requests for comment on the specific allegations described in this report. In earlier statements, authorities have said military operations are conducted in self-defence and that civilians are not deliberately targeted. Political backdrop Violence has escalated since 2025, when opposition leader and first vice president Riek Machar was arrested on charges of subversion, allegations he denies. Machar and President Salva Kiir were once on opposing sides of the country’s 2013–2018 civil war, which killed hundreds of thousands of people before a peace agreement brought them into a fragile unity government. The implementation of that agreement stalled amid delays in unifying armed forces into a national military and repeated postponements of national elections. Following Machar’s arrest, the government undertook a campaign of aerial bombardments to beat back a simmering rebellion in rural areas. Machar’s political group declared the peace deal dead and began launching hit-and-run attacks on military positions. Between December and January, opposition fighters, buoyed by support from local armed youth, seized several military garrisons in Jonglei, prompting the government to announce a counteroffensive on January 28. Then-army chief Paul Nang ordered forces, drawn from the national army, intelligence units, police and allied militias, according to UN investigators, to retake territory held by opposition groups. Analysts say the involvement of allied militias operating alongside formal units has complicated the determination of command responsibility. ‘Burning homes’ Five individuals who fled Lankien told Al Jazeera they witnessed events unfold on February 7. They said government-aligned forces reached the outskirts of the town after fighting in a nearby village. Around late morning, mortar fire struck the town, followed by the arrival of ground forces in armoured vehicles.