Nautilus may refer to:
- HMS Nautilus, a number of ships and a submarine of the Royal Navy
- SMS Nautilus, two ships of the Imperial German Navy and one of the Austro-Hungarian Navy
- USS Nautilus, a number of ships and submarines of the U.S. Navy
- Nautilus (1800), the first practical submarine, built by Robert Fulton in 1800
- Nautilus, the first motorized Staten Island Ferry from 1817
- Nautilus, the Spanish ship commanded by Fernando Villaamil which circumnavigated the world from 1892 to 1894.
- SS Nautilus, formerly Activo, built in Hamburg 1913, used for defence duties in the Arabian Sea during World War II
- MV Nautilus, a 1921 Italian tanker torpedoed in 1942
- SS Nautilus (1922), a German cargo ship lost in a storm in 1962
- Nautilus, formerly USS O-12 (SS-73), an O-11-class submarine (1917–1931) used on Hubert Wilkins's and Lincoln Ellsworth's Arctic Expedition of 1931
- French submarine Nautilus (1930)
- EV Nautilus, an exploration vessel (launched 2009)
- UC3 Nautilus, a privately-built Danish midget submarine (launched 2009, sunk 2017)
- Nautilus, a brig of 60 tons (bm) built at that under the command of Captain Charles Bishop that between 1796 and 1799 sailed in the South Pacific. Bishop purchased her at Amboyna c. November 1796. She visited Tahiti, and then Port Jackson, arriving there in May 1798. From there she sailed to Van Diemen's Land where she took 9000 seal skins before sailing to China. she returned to Port Jackson from China in September 1801, before sailing to Tahiti in May 1802.
- Nautilus, a brig of 185 tons (bm) and 14 guns, launched at Bengal in 1806 for the Bombay Marine. In 1815, after the end of the War of 1812, USS Peacock fired on and captured her, killing and wounding a number of her officers and crew, despite being informed that the war had ended. The Americans released Nautilus when her captain proved that the war had indeed ended. Nautilus was wrecked on the Malabar Coast in 1834.
- Nautilus (Verne), the fictional ship from Jules Verne's novels Twenty Thousand Leagues Under the Sea (1870) and The Mysterious Island (1874)
- Nautilus from Nadia: The Secret of Blue Water anime inspired by Verne's novels
- A fictional submarine as part of the "SCP foundation" collaborative writing project
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