Last Friday, Admiral Alvin Holsey retired two years early at a ceremony in Miami. Tensions have been mounting with Venezuela, including last week's seizure of an oil tanker and nearly 30 deadly strikes on suspected "drug-smuggling" boats.
Three US officials and two people familiar with the matter told Reuters that Holsey was pushed out by Defense Secretary Pete Hegseth. Two officials said Hegseth had grown frustrated with the responsiveness of Holsey and Southern Command.
Donovan's nomination, which was announced by the Pentagon on Friday, will need to be confirmed by the Senate. Lawmakers, including some Republicans, have raised questions about the legality of strikes against suspected drug vessels in the Caribbean.
Donovan's background in special operations suggests the Pentagon's increased focus on potential covert missions in Latin America and follows Trump's pick of the chairman of the Joint Chiefs of Staff, who also hails from the special operations community.
The Pentagon in October established a new counter-narcotics joint task force overseeing operations in Latin America. The task force is led by II Marine Expeditionary Force, a unit capable of rapid overseas operations which is based at Camp Lejeune in North Carolina.
The Trump administration has deployed a force of about 15,000 troops in the Caribbean, including an aircraft carrier, fighter jets and a nuclear-powered submarine.
Trump told NBC News that he was leaving the possibility of war with Venezuela on the table.
Trump this month released his National Security Strategy, arguing that the US should revive the 19th century Monroe Doctrine, which declared the Western Hemisphere to be Washington's zone of influence.
The strategy put the hemisphere at the top of Trump's foreign policy priorities, and alludes to US influence as a way to deny Beijing access to resources such as military installations and critical minerals.