Port Hamilton was surveyed in 1845 by British naval officer Sir Edward Belcher in HMS Samarang and was named after the then secretary of the Admiralty, Captain W. A.
The spacious harbour was also noted for its strategic importance by others, such as Russian Vice-Admiral Yevfimy Putyatin, who visited the islands several times and obtained permission from natives in 1857 to establish a coal depot, though due to delays in the delivery of the coal, the plan was abandoned.
Permission was obtained from China for a cable to be landed at Saddle Island (at the mouth of the Yangtze River).
After the Russian threat had diminished the British demolished the base and left on 27 February 1887, though they continued to frequent the islands, in one case burying a young sailor there.
Until the end of World War II, a Japanese graveyard stood in Port Hamilton.