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Stokes entered the Navy in 1824 and joined the BEAGLE the following year. He served in her for eighteen years, surveying first in South American and then in Australian waters. He was Assistant Surveyor under Robert Fitzroy (1805-1865) during the voyage of 1831 to 1836 and was promoted to lieutenant in 1837. When, in 1841, John Clements Wickham (1798-1864) was invalided during the Australian survey, Stokes took command of the BEAGLE and completed the commission, returning to England in 1843. He was promoted to captain in 1846. From 1847 to 1851 he commanded the ACHERON on the survey of New Zealand. His last employment was in the English Channel survey, 1859 to 1863. He was promoted to rear-admiral in 1864, vice-admiral in 1871 and admiral in 1877.