Alles comes to the Secret Service as the agency is undergoing a review of security around the White House complex and is straining to respond to the logistical difficulties of protecting the Trump family.
In addition to the President, who frequently flies between Washington and South Florida, the first lady and their 11-year-old son live at a private residence in New York, while Trump's grown adult children have business interests that take them around the world.
The Secret Service has asked for US$60 million in additional funding for next year, nearly half of it to protect the Trump family's private home in New York, according to internal agency documents.
Earlier this year, Joseph Clancy announced his plans to step down from his post running the Secret Service, which he took over in 2014 during a period of crisis. The longtime Secret Service veteran was picked by then-President Barack Obama to take over after a series of major security breaches and embarrassing lapses, including a slow response to a gunman who fired at the White House in 2011 and another man who was able to enter the executive mansion.
Alles becomes the newest general - and the latest Marine - to serve in the Trump Administration. Trump selected retired Marine General Jim Mattis to be his Defence Secretary, then asked retired Marine General John Kelly to take over the Department of Homeland Security.
The president had also named Michael Flynn, a retired Army lieutenant general, as his national security adviser, but Flynn resigned this year after his potentially illegal contacts with Russia's ambassador to the United States became public.
To replace him, Trump named army lieutenant general H.R. McMaster. Retired army lieutenant general Keith Kellogg, who served as acting national security adviser until McMaster was picked, is the National Security Council's chief of staff.
The Secret Service director does not need to be confirmed by the Senate.