Fighters of the U.A.E.-trained Security Belt Force, dominated by members of the Southern Transitional Council, patrol an area near the Aden International airport on Wednesday. Photo: nabil hasan/Agence France-Presse/Getty Images

Secretary of State Mike Pompeo urged Yemen’s government and a local faction to resolve their dispute over control of the country’s south, which threatens Saudi-led efforts to reassert control over the entire country and end its war.

The Yemeni faction, called the Southern Transitional Council, fights alongside government forces in a U.S.-backed international coalition led by Saudi Arabia against the Iran-aligned Houthi rebels in the country’s north, but it is also seeking a separate state in the south.

Their rival agendas for Yemen have often resulted in clashes, and three weeks ago the STC captured the government’s interim capital, Aden. On Wednesday the two sides fought for control over the port city, with both claiming the upper hand. The clashes have exposed deep rifts in the coalition and threaten to splinter it.

“Very important for the unity, stability, and prosperity of Yemen that the Yemeni government and STC resolve their dispute,” Mr. Pompeo said in a tweet, after meeting Khalid bin Salman, the Saudi vice defense minister and brother of Crown Prince Mohammad bin Salman.

“Had a productive meeting with @kbsalsaud today to discuss #Yemen, maritime security, countering the Iranian regime’s dangerous activities, and human rights,” Mr. Pompeo said.

Prince Khalid is leading a Saudi delegation in the U.S. to discuss bilateral relations and issues related to regional security and stability, according to the official Saudi Press Agency. Washington is looking to nudge Riyadh into taking part in secret talks with Houthi leaders in an effort to broker a cease-fire in Yemen, The Wall Street Journal reported this week.

But in an indication of the tough challenge of bringing them together, both the Hadi government and the STC claimed to have control over Aden on Wednesday.

Yemen’s President Abed Rabbo Mansour Hadi, right, meets with the U.N. envoy to Yemen Martin Griffiths, on July 10 in Aden, before the government lost control of the city to its rival ally, the STC. Photo: Ismail Rabidhy/Xinhua/Zuma Press

Yemen’s Minister of Information Moammar al-Eryani said government soldiers and presidential guards had secured Aden and its surroundings. The government broadcast footage and photos from Wednesday of its soldiers in the streets of the port city.

In a videotaped speech from Aden, one of the STC officers, Maj. Gen. Ahmed bin Breik, claimed the rebels were still in full control of the city.

The most recent fighting erupted after STC fighters seized the presidential palace in Aden on Aug. 10. Saudi Arabia called for a cease-fire between the two ostensible allies. Forces loyal to President Abed Rabbo Mansour Hadi refused to meet with the rebels and instead launched the current offensive.

“The National Army & the security forces impose full control over Aden districts amid great public satisfaction and welcome,” Mr. Eryani said on Twitter. He added that government forces were pardoning rebels so they could redeploy within the coalition.

The government said its forces on Wednesday also pushed STC fighters out of the capital of the southern Abyan province. STC had taken the capital, Zinjibar, days after seizing Aden.

STC had previously accepted the invitation to talks in Jeddah, Saudi Arabia, and said it captured Aden to draw international attention to its quest for self-determination in the south.

After the group took the port city, the Riyadh-backed Hadi government demanded that the United Arab Emirates, which arms and trains the STC, be expelled from the coalition altogether. Mr. Hadi’s government even threatened to complain to the United Nations about alleged abuses of Yemenis in U.A.E.-run secret prisons in southern Yemen. The U.A.E. denied the charges.

The U.A.E. has in recent weeks begun extricating itself from the Yemen war, withdrawing tanks, attack helicopters and hundreds of soldiers. However, it continues to support the STC, which gives Abu Dhabi influence particularly in southern Yemen.

The friction within the anti-Iran coalition has jeopardized United Nations-led efforts to de-escalate the conflict by opening up a new, potentially long-lasting front in the war. The government said a divided coalition also benefited the Houthis.

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