Hegseth announced Holsey's retirement on X without giving a reason.
He praised the four-star admiral and first Black commander of SOUTHCOM for having "exemplified the highest standards of naval leadership" and for his "unwavering commitment to mission, people and nation."
"His tenure as Military Deputy Commander and now Commander of United States Southern Command reflects a legacy of operational excellence and strategic vision," Hegseth said in the statement.
"The Department thanks Admiral Holsey for his decades of service to our country, and we wish him and his family continued success and fulfillment in the years ahead."
In a statement of his own, Holsey said his retirement will be effective Dec. 12.
"It has been an honor to serve our nation, the American people and support and defend the Constitution for over 37 years," he said.
"The SOUTHCOM team has made lasting contributions to the defense of our nation and will continue to do so. I am confident that you will forge ahead, focused on your mission that strengthens our nation and ensures its longevity as a beacon of freedom around the globe."
Holsey's announcement comes less than a year after he assumed the position in November. He took over from Gen. Laura Richardson, the first woman to lead SOUTHCOM, who also retired.
Military leadership has undergone a shake-up under the second iteration of the Trump administration, with several senior generals and admirals either fired, replaced or retired since January.
A day after his inauguration, Trump dismissed Adm. Linda Fagan, the first woman to serve as commandant of the U.S. Coast Guard.
In February, Trump fired Air Force Gen. Charles Q. Brown Jr. as chairman of the Joint Chiefs of Staff and Adm. Lisa Franchetti as chief of Naval Operations.
Then in April, he fired Gen. Timothy Haugh, head of the National Security Agency.
In August, Gen. David Allvin announced he was retiring early as the U.S. Air Force chief.
The announcement of Holsey's retirement comes as President Donald Trump directed a series of military attacks targeting alleged Venezuelan drug trafficking boats in the Caribbean Sea.
At least 27 people have been killed in the half-dozen attacks since they began on Sept. 2.
Trump and his administration have said intelligence supports their actions, while critics argue that using the military to strike civilian noncombatants may violate U.S. and international law.
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