John Jones, widely known as Johnny Jones, was born probably in Sydney, New South Wales, in 1808 or 1809, the son of Thomas Jones; his mother's name is unknown. He spent his early years in sealing and whaling ships, probably visiting the coast of New Zealand, until he became a waterman, ferrying people across Port Jackson (the harbour of Sydney). On 7 January 1828, at Sydney, he married Sarah Sizemore; they were to have 11 children.
By 1830 Jones had purchased shares in three whaling vessels, and in 1835 went into partnership with Edwin Palmer to purchase a whaling station at Preservation Inlet, New Zealand, and a schooner, the Sydney Packet, for whaling. Acquiring further sailing vessels, he gained a controlling interest in most southern New Zealand whaling stations, employing about 280 men on seven stations. In 1838 he bought from two insolvent Sydney merchants a whaling station and a quantity of land near Waikouaiti for £225. To look after his business interests as well as his medical needs, he persuaded Dr Joseph Crocome to leave George and Edward Weller's whaling station at Otago (Ōtākou) for Waikouaiti.
Jones's initial success led him, in 1838, to buy from the Ngāi Tahu leader Tūhawaiki blocks of land in the regions that became known as South Otago and Southland. In 1839 he purchased a further block, indefinitely bounded, but stretching ostensibly from Waikouaiti to Lake Wanaka. In 1840 he brought Tūhawaiki, Karetai, Taiaroa and other Māori to Sydney; George Gipps, governor of New South Wales, invited them to sign a treaty ceding sovereignty of their lands to the Crown. Jones was aware that his landholdings were in danger if the South Island became a British possession, and persuaded the chiefs not to sign. He, along with William Charles Wentworth and three other Sydney entrepreneurs, then purchased all unsold land in the South Island for £200. Gipps refused to recognise the validity of the purchase, and Jones was later granted only the allowable maximum of 2,560 acres. After persistent petitioning for an extension of the award, he was allowed an additional 8,650 acres, but not until 1867 were his long-standing land claims finally settled.
Meanwhile Jones provisioned his Waikouaiti station from Sydney. In 1840 he became the first to bring organised settlement to the east coast of the South Island, when he settled near his whaling station about a dozen families from Sydney, to grow crops and to care for sheep, cattle and horses, which he exported from New South Wales, thus establishing the first farm in Otago. To help maintain a semblance of moral order in an otherwise lawless community he secured in 1840, through the Wesleyan Board in Sydney, the services of the Reverend James Watkin, whom he settled with his family at Waikouaiti. Watkin, however, remained for only four years before being succeeded by the Reverend Charles Creed in 1844.
The failure of the Waikouaiti settlement to prosper, together with losses incurred during a depression in Sydney, forced Jones to move with his family to New Zealand in 1843. He divided his time between Waikouaiti and Wellington and traded between New Zealand ports and Sydney with his schooner Scotia. He ceased to operate from Wellington after the earthquake of 1848. The decline of whaling forced him to close his Waikouaiti station, and he concentrated on developing his farm. Under his benevolent despotism the settlement recovered. Far removed from the watchful eye of government, he enforced his own rough notions of justice with a strong right hand. He concentrated on food production at nearby Cherry Farm (where in 1862 he built a flour mill), to supply not only the Waikouaiti community but also Dunedin. There, in anticipation of the arrival of the first settlers of the Otago Association in 1848, he established a small trading store, to become their chief supplier of foodstuffs.
Jones's widening commercial interests and his children's educational needs led him to move in 1854 to Dunedin, where he bought a large house, Fernhill, from Captain Edmund Bellairs. The engagement of a tutor, the Reverend Henry Graydon Johnston, was, however, short-lived, owing largely to Jones's fiery temper. His trading interests brought him into competition with the rising businessman James Macandrew, whose entry into the coastal trade in 1851 ended Jones's monopoly. The two rivals also competed in the issue of promissory notes, until the Union Bank of Australia opened a Dunedin branch in 1857. Jones softened the impact of the slump of 1866 by charging only 10 per cent on mortgages, at a time when others were charging 15 and 20 per cent.
But shipping was Jones's main interest. He purchased the brig Thomas and Henry in 1854, and in 1858 entered into partnership with two sons of William Cargill, John and Edward, operating the paddle-steamer Geelong. In 1863 he became a shareholder in the Otago Steam Ship Company. Unfortunately, through undercapitalisation, bad management and misfortune at sea, the company went into voluntary liquidation in 1864. Along with fellow shareholders he purchased the assets through another of his ventures, the Harbour Steam Navigation Company, which was formed to serve the Dunedin–Port Chalmers–Ōamaru trade. With three steamers the company later extended its services to Hokitika and Ōkārito on the West Coast.
Beyond his business activities, Jones had few other interests. He took little part in politics, realising no doubt his own limitations, and refused a seat, offered by the Stafford ministry, on the Legislative Council. In 1856 he resigned his commission as a justice of the peace, an office he had held since 1854. He headed a syndicate which in 1851 published the Otago Witness, was chairman of the Dunedin Town Board in 1856, and in the same year helped to form the Otago Constitutional Association to protect the interests of squatters against the provincial council. Of uncertain religious affiliation, he was determinedly non-sectarian, building and endowing the Anglican church at Waikouaiti in 1858, making land grants and donations to the Presbyterian, Catholic and Methodist communities, and giving to the Anglican community in Dunedin the land on which St Paul's Cathedral was eventually built.
Johnny Jones died in Dunedin on 16 March 1869, outliving Sarah Jones by five years. By sheer courage, determination and hard work, he rose to a position of leadership. All feared his ungovernable and impetuous temper, yet he was known to be generous, and kindly towards women and children. Temperate in his habits and scrupulously fair in his dealings, he was a unique product in a pioneer society.