U.S. General Joseph F. Dunford (right) pictured with former NATO commander U.S. General John Allen in Kabul.

Story highlights

Marine Gen. Joseph Dunford replaces Gen John Allen as ISAF commander

Dunford will over the final two years of the war and the withdrawal of troops

Dunford assumed command during a ceremony in Kabul

U.S. Marine Gen. Joseph Dunford took command Sunday of the NATO-led International Security Assistance Force in Afghanistan, where he will oversee the final two years of the war and the withdrawal of nearly all troops.

“Today is not about change, it’s about continuity,” Dunford said at a change-of-command ceremony in Kabul attended by his predecessor Marine Gen. John Allen and other senior NATO and Afghan officials.

“I’ll endeavor to continue the momentum of the campaign and support the people of Afghanistan as they seize the opportunity for a brighter future.”

Dunford replaces Allen, whose final days as ISAF commander were marred by an investigation linked to the scandal that led to the resignation of his predecessor David Petreaus as the director of the CIA.

Allen, who has been nominated as NATO’s supreme allied commander, was cleared in January of allegations he wrote potentially inappropriate emails to a Florida woman who claimed she was being threatened by Petreaus’ mistress Paula Broadwell.

Allen oversaw perhaps one of the toughest periods for U.S.-led NATO troops as they battled an ever-evolving insurgency while balancing combat with diplomacy.

Reports routinely emerged of prickly relations between Allen and Afghan President Hamid Karzai, who did not attend the ceremony. It not uncommon for a head of state to skip a military handover ceremony.

Meanwhile, Afghan Defense Minister Bismillah Mohammadi credited Allen for a drop in civilian casualties in Afghanistan, saying it helped to restore public confidence in the government.

Until Dunford’s name emerged in August as the nominee for the top job in Afghanistan, few people outside of the military community, had heard of him.

Dunford has a reputation among Marines as a thoughtful, calm leader with more than 22 months under his belt of commanding troops in Iraq.

The general has no real Afghanistan-ground experience. But his is not the first ISAF commander to be in that position. Before then-Army Gen. David Petreaus took over ISAF command, he had overseen the war in Afghanistan from his perch as chief of Central Command in the United States.

Chief among the issues Dunford faces is an Afghan government that has, at times, been critical of NATO forces and their actions in Afghanistan.

Afghan security forces, considered the key to the country’s success when troops withdraw by the end of 2014, still have a long way to go before they are able to handle some operations without the help of the international forces.

He also faces the issue of Afghanistan’s ongoing insurgency, including the attacks that continue to be carried out by Taliban militants and the Haqqani Network.

But officials close to Dunford have told CNN that the general is not going into the job blind. Since August, he has been studying the history of Afghanistan as well as the military operations since the war began in 2001, said the officials, who spoke on condition of anonymity because they were not authorized to release the information.

CNN’s Mike Mount and AnneClaire Stapleton contributed to this report.