The head of the New York Army National Guard’s storied “Irish Brigade” relinquished his command during a ceremony at the 69th Regiment Armory in Manhattan Thursday, shortly after leading his 1,000-man unit in the city’s St. Patrick’s Day Parade.

Lt. Col. Sean Flynn is moving on to become executive officer of the 27th Infantry Brigade Combat Team, based in Syracuse.

“Lt. Col. Flynn has the blood of this unit in his veins,” Col. Joseph Biehler, who commands the combat team that Flynn is joining, said during a brief ceremony before troops at the armory.

Flynn’s replacement is Lt. Col. Don Makay of Brooklyn. Makay served more than a dozen years in the active duty Army — including leadership positions within the 101st Airborne Division — and has fought in Iraq, Afghanistan and Kosovo.

During a brief farewell address to his troops, Flynn reserved special praise for the 69th’s sergeants, whom he credited with drilling the unit’s younger soldiers “repetitively under live fire conditions so as to insure they are ready to close the last 100 yards, the most dangerous mission of the infantry.”

“It is an honor to command any soldiers, but it is a distinct honor to command this most American of battalions, which represents everything in America that is good,” Flynn said.

Before taking command of the 69th Infantry Regiment in January 2014, Flynn, 43, had endeared himself to many of his troops after taking command of the 69th’s Long Island-based Bravo Company, beginning in 2003.

That would prove to be a key point in his career. He was a 31-year-old National Guard officer that next year, when his unit of part-time soldiers was ordered into combat for the first time since World War II.

Soldiers from the 69th would patrol the Baghdad suburbs and the deadly “Route Irish” highway to the airport, both of which were rife with insurgent activity and makeshift bombs. In all, 19 soldiers were killed during the yearlong deployment.

Flynn, who lives in Delmar, said understanding that his ability to train men for combat could spell the difference between whether they lived or died steeled him as a leader.

He said he oversaw 10-year anniversary graveside memorial services for each of the 69th’s soldiers who perished during the 2004-2005 deployment, reuniting families with men their loved ones had fought alongside.

He grew pensive when asked what he thinks his legacy with his unit would be.

“Poets and novelists can define that better,” he said. “But I hope that as commander I have prepared my soldiers ensure that when they go to fight again — and there is no doubt there will be another time — that they are as prepared as possible for the challenges of combat.”

CORRECTION: An earlier version of this story gave the wrong first name of Sean Flynn.

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