Original: On 9 September 1839, HMS Beagle sailed into Darwin harbor during its surveying of the area. John Clements Wickham named the region "Port Darwin" in honor of their former shipmate Charles Darwin, who had sailed with them on the ship's previous voyage which had ended in October 1836.
Simplified: A member of the crew of the ship that started a port there in 1839 named it Port Darwin in honor of Darwin, who had sailed on that same ship earlier.