None, he was a naturalist, not a sea captain. He sailed on the HMS Beagle captained by Robert FitzRoy.
Yes, the first European ship to see Darwin harbour was the Beagle and her captain (John Clements Wickham) named it after Charles Darwin - Wickham had sailed with Darwin on the famous 2nd voyage of the Beagle.
The captain of the Beagle was Robert FitzRoy. He was a British naval officer who captained the ship during Charles Darwin's famous voyage around the world from 1831 to 1836.
HMS Beagle
Charles Darwin at age 22 embarked on a voyage on a ship called the Beagle, as ships naturalist and companion to the ships captain. The voyage was suppose to last 2years but did not return to England for five years.
Captain Robert FitzRoy was the captain of the HMS Beagle during its most famous voyage, which included Charles Darwin as the ship's naturalist. FitzRoy and Darwin were instrumental in conducting research and mapping the coast of South America during this expedition.
The HMS Beagle was the ship that carried Charles Darwin on his famous five-year voyage from 1831-1836.
The Beagle
Farley chox
It wasn't his personal ship, it belonged to the Royal Navy - it was called HMS Beagle.
Charles Darwin visited Floreana, Isabela, San Cristóbal, and Santiago islands
the beagle
H.M.S Beagle