This is a list of ships that were assigned to the Royal Navy's Australian Squadron between 1859 until 1913. The Australian Squadron was replaced by the Royal Australian Navy Fleet when it sailed into Sydney Harbour on 4 October 1913.[1]
| Ship | Date joined | Date left | Notes |
| HMS Iris | 25 March 1859 | 1861 | Flagship between 25 March 1859 until 10 March 1860. Undertook operations during First Taranaki War in New Zealand. |
| HMS Pelorus | May 1859 | July 1862 | Flagship between 10 March 1859 until July 1862. Undertook operations during First Taranaki War. |
| HMS Niger | 25 March 1859 | 1860 | Undertook operations during First Taranaki War. |
| HMS Cordelia | 1859 | December 1860 | Undertook operations during First Taranaki War. |
| HMS Elk | 1859 | 1860 | Undertook operations during First Taranaki War. |
| HMS Bramble | 1859 | May 1859 | Tender to Squadron. |
| HMS Miranda | December 1860 | September 1864 | Undertook operations during Invasion of Waikato and also the Tauranga Campaign in New Zealand. |
| HMS Pioneer | March 1862 | 1863 | |
| HMS Fawn | April 1860 | August 1862 | |
| HMS Harrier | December 1860 | September 1864 | Participated in rescue operation when HMS Orpheus was wrecked in Manukau Harbour, New Zealand and was also grounded but was refloated. Undertook operations during Invasion of Waikato and also the Tauranga Campaign in New Zealand. |
| HMS Orpheus | July 1862 | 7 February 1863 | Flagship between July 1862 until 7 February 1863. Was wrecked in Manukau Harbour with the loss of 189 seaman including Commander-in-chief, Australia Station Commodore William Farquharson Burnett. 70 crewman survived. |
| HMS Eclipse | November 1862 | 1866 | Undertook operations during Invasion of Waikato and also the Tauranga Campaign. |
| HMS Beatrice | September 1862 | 1880 | Jointly owned by Royal Navy and Colony of South Australia until purchased outright by South Australia in 1880. Conducted survey operations around Northern Australia. |
| HMS Curacoa | 20 April 1863 | 1866 | Flagship from 20 April 1863 until May 1866. Undertook operations during Invasion of Waikato and also the Tauranga Campaign. |
| HMS Esk | July 1863 | 2 July 1867 | Undertook operations during Invasion of Waikato and also the Tauranga Campaign. |
| HMS Brisk | October 1864 | 1868 | Provided escort for operations during Second Taranaki War, New Zealand. |
| HMS Salamander | February 1864 | 4 July 1867 | Conducted survey operations along Great Barrier Reef and between Wilsons Promontory and Port Phillip Bay. |
| HMS Hecate | June 1863 | 1864 | Conducted survey operations of Botany Bay, Moreton Bay and Brisbane River. |
| HMS Falcon | December 1863 | November 1867 | Undertook operations during Invasion of Waikato and also the Tauranga Campaign. |
| HMS Challenger | May 1866 | 1870 | Flagship between May 1866 and 3 September 1870. Conducted a punitive operation in 1866 against some Fijian natives. |
| HMS Charybdis | March 1867 | November 1868 | |
| HMS Blanche | January 1868 | 1875 | Undertook a punitive operation in 1869 against some Soloman Islands natives. Conducted survey operations of Rabaul Harbour. |
| HMS Virago | 30 November 1866 | 28 June 1871 | Conducted survey operations along Great Barrier Reef, Queensland, Norfolk Island and New Zealand. |
| HMS Rosario | November 1867 | 1875 | Undertook anti-blackbirding operations in the South Pacific. |
| HMS Clio | 17 April 1870 | 16 October 1873 | Flagship between 3 September 1870 and 17 September 1873. Ran into a reef and holed in Bligh Sound, New Zealand in 1871 and repaired. |
| HMS Cossack | September 1871 | October 1873 | |
| HMS Dido | 1871 | 1875 | Ran aground at Hobart, Tasmania in 1875 but was refloated. |
| HMS Basilisk | March 1871 | 1874 | Undertook survey operations around Eastern New Guinea, under the command of Captain John Moresby. Undertook anti-blackbirding operations in the South Pacific. |
| HMS Alacrity | 1873 | 1882 | Built in Sydney as Ethel. Undertook survey operations around Fiji and Soloman Islands. Sold to Colony of New South Wales and served as a powder hulk. |
| HMS Beagle | 1873 | March 1883 | Built by John Cuthbert, Darling Harbour, Sydney. Undertook anti-blackbirding operations in the South Pacific. In 1879 undertook punitive operation in against some Soloman Islands natives. |
| HMS Conflict | August 1873 | 1882 | Built by John Cuthbert, Sydney. Undertook anti-blackbirding operations in the South Pacific. In 1879 undertook punitive operation in against some Soloman Islands natives. |
| HMS Renard | 1873 | March 1883 | Built by John Cuthbert, Sydney. Undertook anti-blackbirding operations in the South Pacific. Undertook survey operations around Fiji and Russell Islands. |
| HMS Sandfly | 1873 | 1883 | Built by John Cuthbert, Sydney. Undertook anti-blackbirding operations in the South Pacific. Undertook survey operations around Soloman Islands and New Guinea. Commanding officer, Lieutenant Bower, and three sailors were killed by natives on Mandolina Island, near Guadacanal. |
| HMS Pearl | 22 May 1873 | 1875 | Flagship from 17 September 1873 until 7 September 1875. Commander-in-chief Commodore James Graham Goodenough and two sailors died from poisonous arrows fired by natives from Santa Cruz Islands in 1875. |
| HMS Nymphe | March 1875 | November 1878 | |
| HMS Barracouta | August 1874 | July 1866 | Participated in Samoan Operations in 1866. |
| HMS Sappho | December 1874 | August 1878 | |
| HMS Wolverine | 7 September 1875 | January 1882 | Flagship from 7 September 1875 until 21 January 1882. Sold to Colony of New South Wales and served as a training ship. |
| HMS Emerald | July 1868 | October 1881 | Took punitive action against natives who killed commander of HMS Sandfly. |
| HMS Diamond | October 1881 | August 1888 | |
| HMS Sapphire | March 1875 | July 1879 | |
| HMS Danae | 1878 | August 1880 | |
| HMS Cormorant | 1878 | 1882 | Took punitive action against natives who killed commander of HMS Sandfly. |
| HMS Espiegle | November 1881 | March 1885 | |
| HMS Miranda | September 1880 | May 1886 | |
| HMS Alert | 1880 | 1882 | |
| HMS Meda | 1880 | 1886 | Undertook survey work along North West Australia. She was sold in 1887 to the Colony of Western Australia. |
| HMS Nelson | 21 January 1882 | 3 September 1888 | Flagship from 21 January 1882 until 1888. |
| HMS Calliope | September 1887 | October 1889 | Participated in the 1889 Samoan conflict. |
| HMS Opal | March 1885 | 11 May 1890 | |
| HMS Rapid | July 1886 | 1 December 1897 | |
| HMS Egeria | 1887 | 1894 | She undertook survey work around Western Pacific islands and Hobart. |
| HMS Flying Fish | 1866 | 1866 | |
| HMS Myrmidon | 14 March 1885 | 1888 | Undertook surveys along the North of Australia, Darwin and Bass Strait. |
| HMS Dart | 1883 | 1904 | |
| HMS Raven | 25 April 1883 | October 1890 | |
| HMS Swinger | 2 October 1883 | August 1891 | |
| HMS Paluma | 1884 | 1895 | Built for Colony of Queensland, she was commissioned in Royal Navy on loan. She was returned to Queenland in 1895 and renamed HMQS Paluma. |
| HMS Undine | September 1883 | 1888 | |
| HMS Lark | 1882 | 1886 | |
| HMS Harrier | September 1883 | 1888 | |
| HMS Orlando | 1888 | 1898 | Flagship from 1 September 1888 until November 1897. |
| HMS Katoomba | 24 March 1891 | January 1906 | Part of the auxiliary squadron. |
| HMS Mildura | 18 March 1890 | 1905 | Part of the auxiliary squadron. |
| HMS Ringarooma | 3 February 1891 | 1904 | Grounded on a reef at Malekula Island, New Hebrides on 31 August 1894 and was towed off by a French warship. Part of the auxiliary squadron. |
| HMS Tauranga | 27 January 1891 | 1904 | Part of the auxiliary squadron. Participated in the 1899 Samoan civil war. |
| HMS Wallaroo | 31 March 1891 | January 1906 | Part of the auxiliary squadron. Participated during the Boxer Rebellion in 1900. One of her boilers exploded on 7 January 1904 killing 4 sailors. |
| HMS Boomerang | 1891 | 1904 | |
| HMS Karrakatta | 1891 | 1903 | |
| HMS Cordelia | 1890 | 1891 | During practise firing one of her guns burst killing five sailors on 28 June 1891. |
| HMS Curacoa | 1890 | December 1894 | |
| HMS Mohawk | December 1897 | 1900 | Escorted New South Wales Naval Brigade to China during the Boxer Rebellion in 1900. |
| HMS Porpoise | December 1897 | June 1901 | Participated in the 1899 Samoan civil war. |
| HMS Pylades | November 1894 | 29 January 1905 | |
| HMS Royalist | May 1888 | June 1899 | Participated in the 1899 Samoan civil war. |
| HMS Penguin | 14 January 1890 | 1888 | She undertook survey work around Western Pacific islands, New Zealand and Great Barrier Reef. She was transferred for harbour service at Sydney before being commissioned into the RAN as HMAS Penguin a depot ship. |
| HMS Torch | February 1897 | 1913 | |
| HMS Rambler | October 1889 | 1890 | She undertook survey work along North Western coast of Australia. |
| HMS Goldfinch | March 1890 | August 1899 | |
| HMS Ringdove | 1891 | February 1901 | |
| HMS Lizard | January 1889 | 1904 | Participated during the Boxer Rebellion in 1900. |
| HMS Royal Arthur | 4 November 1897 | 1888 | Flagship from 4 November 1897 until April 1904. |
| HMS Phoebe | 19 February 1901 | 23 December 1905 | |
| HMS Psyche | 22 September 1903 | 1913 | Was later commissioned in RAN in 1915 as HMAS Psyche. |
| HMS Archer | 1900 | December 1901 | |
| HMS Mutine | December 1903 | February 1905 | |
| HMS Sparrow | February 1901 | 1904 | |
| HMS Waterwitch | 1895 | 1900 | |
| HMS Euryalus | July 1904 | 1905 | Flagship between 26 March 1904 and February 1905. |
| HMS Challenger | 1904 | 1912 | |
| HMS Cadmus | 13 April 1904 | May 1905 | |
| HMS Clio | 19 January 1904 | 14 April 1905 | |
| HMS Powerful | February 1905 | December 1911 | Flagship between 1905 until 1911. |
| HMS Encounter | December 1905 | 21 June 1912 | Commissioned as HMAS Encounter on 1 July 1912. |
| HMS Cambrian | 1905 | 1913 | Flagship between January and October 1913, the last flagship of Australia Station |
| HMS Pegasus | March 1905 | March 1913 | |
| HMS Pioneer | September 1905 | 1 March 1913 | Commissioned as HMAS Pioneer in 1913. |
| HMS Prometheus | 1905 | 1913 | |
| HMS Pyramus | 16 September 1905 | 1913 | She grounded on a reef near Cooktown on 22 June 1907 and was refloated. |
| HMS Fantome | 1906 | 1913 | Undertook survey work along the North and Eastern coasts of Australia and New Guinea. |
| HMS Sealark | 1910 | 1913 | Undertook survey work in the Torres Strait and Soloman Islands. |
| HMS Drake | 30 November 1911 | 1 January 1913 | Flagship between 1911 and 1 January 1913. |