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Johnstone entered the Navy in 1858 and served on the Mediterranean Station and then in the ST GEORGE between 1860 and 1864. He was promoted to lieutenant in 1865. From this time until 1873 he served on the China Station in the SERPENT, PERSEUS and JUNO, was then appointed to the command of the training brig LIBERTY. He was made a commander in 1877. Afterwards he commanded the EGERIA in China and the DRYAD in the East Indies; in both ships he was involved in diplomatic affairs in Borneo and then in Madagascar, for which service he was promoted to captain in 1883. He attended the Royal Naval College, Greenwich, and subsequently served on a committee inquiring into the education of naval officers. From 1885 to 1889 he commanded the VOLAGE in the Training Squadron. In 1891 he took command of the AGAMEMNON and turned over with his crew to the CAMPERDOWN the following year; he was still in command when the CAMPERDOWN collided with the VICTORIA, for which incident he was held partly to blame by the Admiralty. His only service after this was as Flag-Captain to the Commander-in-Chief, Devonport, 1896 to 1898. He retired as rear-admiral in 1899 and became a vice-admiral in 1903.