
The president said the small boat, which was sailing in international waters, was carrying drugs to the United States.
Trump said three people were killed in a raid on "violent drug traffickers," but offered no evidence that the boat was carrying drugs.
The attack came after Venezuelan President Nicolas Maduro said his country would defend itself against a US "invasion".
Maduro called US Secretary of State Marco Rubio a "lord of death and war".
Relations between the two countries have been strained since the US launched a counter-narcotics operation in the southern Caribbean a few weeks ago, killing 11 people.
"This morning, at my direction, the United States military conducted a second strike against the rebellious and violent drug traffickers," Trump wrote on Twitter.
Trump also shared a 30-second video showing a small boat on the ocean being destroyed by the attack.