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 . 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 .