FitzRoy entered the British Navy in 1819, aged 14. Promotion was rapid; this was probably due as much to his aristocratic descent (his grandfather was Augustus Henry Fitzroy, 3rd Duke of Grafton) as to his undoubted ability. In 1823 he was given command of the hydrographic survey ship, HMS Beagle and soon established his reputation as a navigator, scientist and commander.
In 1831 he set out on his most famous voyage, a five year circumnavigation of the world. His resident naturalist was Charles Darwin who described the journey in Voyage of the Beagle. Darwin used the observations he made during this period as the basis on which he formulated his Theory of Evolution. Darwin described FitzRoy as a man of considerable charm with liberal views, i.e. open minded.
FitzRoy was awarded a gold medal by the Royal Geographical Society in 1837, and became a Member of Parliament in 1841 and Conservator for Merseyside in 1842.
The first Governor of New Zealand, William Hobson, died in late 1842 and the Church Missionary Society, which had a strong New Zealand presence, suggested FitzRoy as his successor. He took up his new task in April 1843.
It was probably an impossible job. His instructions were to maintain order, protect the Maori and yet to satisfy the land hunger of the settlers pouring into the country. He was given very few military resources and very little revenue, mainly from customs duties.
One of his first tasks was to enquire into the circumstances surrounding the Wairau Massacre. He found the actions of the Colonists to have been illegal and wisely declined to take any action against Te Rauparaha, wisely because he didn't have the troops to meet him on anything like equal terms. However this left the New Zealand Company and the Settlers feeling betrayed and angry. One outcome though was to appoint a Government Superintendent for the area and establish a ruling presence. He also insisted that the piratical New Zealand Company pay the Maori a realistic price for the land they claimed to have purchased. Naturally these moves made him very unpopular.
Land sales were a continuing vexatious issue. The Maori wanted to sell land and the settlers wanted to buy land but according to the Treaty of Waitangi this could only happen with the Government as an intermediary and this proved to be very slow. FitzRoy changed the rules to allow the direct purchase of Maori land subject to a duty of ten shillings per acre, $2.50 per hectare.
However land sales proved slower than expected. To meet the financial shortfall FitzRoy raised the customs duties then he abolished them and instituted a property and income tax. However nothing really worked and quite soon the Colony was faced with bankruptcy and FitzRoy was forced to begin issuing promissory notes, paper money without backing.
Meanwhile the Maori in the Far North, the Bay of Islands, who had been one of the driving forces in the signing of the Treaty of Waitangi, were feeling increasingly sidelined and resentful of the changes that had taken place in New Zealand. To signal their resentment Hone Heke cut down the flagpole at Kororareka. Rather than address the problems FitzRoy had the flagpole re-erected. Hone Heke cut it down again, four times altogether by which time the First New Zealand War, or Flagstaff War, was well underway.
It soon became apparent that FitzRoy did not have the resources to bring about a quick end to the war. Meanwhile the spokesmen for the New Zealand Company were active back in Great Britain and FitzRoy's Governorship was presented to the House of Commons in a very poor light. As a result of this he was dismissed and replaced by George Grey then Governor of South Australia. Grey was also given the backing and support that FitzRoy had needed but was denied.
However FitzRoy was not disgraced. He returned to England and became superintendent of the Royal Naval Dockyards at Woolwich and then later command of HMS Arrogant. He was elected to the Royal Society in 1851 and then later became the first director of the new meteorological service (now the Meteorological Office) for the Board of Trade.
He retired in 1863 as a Vice Admiral and died by suicide two years later. FitzRoy was devout Christian and as such he found Darwin's Theory of Evolution objectionable and strongly opposed it.