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The Aboriginal inhabitants of the Melbourne region made use of many indigenous plants and engaged in horticultural practices, aerating the soil by digging, thinning out plants, fertilising with ash and spreading cultivars by trading. European settlers at Port Phillip brought with them fruit trees, vegetables and ornamental plants, which generally flourished in the local soils and climate. Subsistence farms gave way to more specialised market gardens, orchards and vineyards with the Western Market reserved in 1841 for sale of horticultural produce. Early nurseries stocked a surprisingly large range of plants. John Pascoe Fawkner's nursery and orchard in Pascoe Vale (Pascoeville), for example, advertised 35 varieties of apple, 20 of pear, 20 of plum, 10 of cherry, over 200 varieties of grapevine, assorted peaches, nectarines, apricots, figs, currants, mulberries, gooseberries, trees, shrubs and bulbs in 1848. Charles Stone established the first nursery in Brighton in the 1860s and by 1887 there were five others, including that of Richard Cheeseman, the first president of the National Association of Nurserymen and Seedsmen. The long-running Brunnings nursery was established in St Kilda in 1887, moving later to South Melbourne.

In the 1850s Melbourne and the gold diggings provided a good market for horticultural crops. Small market gardens and orchards were established in inner suburbs like Hawthorn and large estates also carried horticultural produce. In 1855 St Ninians in Brighton devoted 8 acres (3.2 ha) to fruit and vegetables and vineyards flourished in Boroondara, Prahran and Brighton. Following the 1860s Land Acts selectors cleared land for horticultural purposes in outlying parishes such as Nunawading.

In 1865 the South Bourke Standard newspaper reported that gardens and nurseries had been struck by blight, aphis, red spider, caterpillars and drought and the Collector of Agricultural Statistics noted that agriculture in Nunawading was struggling due to poor land, dry conditions and intermittent flooding. Many Chinese who came to Melbourne in the 1870s and 1880s turned to market gardening, continuing well into the 20th century. It has been claimed that the impetus behind the formation of a Market Gardeners and Fruit Growers Association in 1900 was concern about 'unfair competition' from Chinese gardeners.

Horticultural crops were not restricted to food items. In the 1860s damask roses and poppy heads were harvested for perfumes in Nunawading which also boasted a violet farm while daffodils and boronia flourished in Blackburn South. In 1909 the Adult Deaf and Dumb Society established a large mixed flower farm in Blackburn, and the flowers were sold at the Melbourne Flower Market.

After World War II orchardists and market gardeners were driven out by increasing taxes and rates. Only a few continued into the 1980s, though in 1988 the City of Nunawading acquired 6 acres (2.4 ha) of the area's last remaining orchard as an Australian bicentennial project. Wholesale nurseries increased in number until about 1920 when the total acreage began to decline. Although they have virtually disappeared from the inner suburbs, there are an increasing number of retail nurseries and garden centres.

Horticulture as entertainment has long been a feature of Melbourne with regular shows and exhibitions being held from the 1850s. In 1848 the Victorian Horticultural Society was formed after a public meeting in the Queens Head Hotel to 'further horticultural activity and knowledge'. John Pascoe Fawkner became secretary and Charles La Trobe an official patron. The society appears to have been inactive between 1851 and 1855, and in 1856 was replaced by the Horticultural Society of Victoria (HSV, later the Royal Horticultural Society, RHSV). The Society continues to cater for both professional and amateur horticulturalists. The Victorian Horticultural Improvement Society combined with the HSV for an exhibition in 1863. Other local societies were formed, for example, the Brighton Horticultural Society in 1856. Later, garden clubs were formed in many suburbs including Caulfield, Carrum, Doncaster, Frankston, Altona and Ivanhoe. The Council of the Horticultural Societies and Garden Clubs of Victoria was established in 1975.

Melbourne is home to many specialist societies: the Rose Society of Victoria (1899), the Victorian branches of the Australasian Native Orchid Society as well as various local orchid clubs and societies, the Australian Rhododendron Society, the Australian Camellia Research Society, the Australian Giant Pumpkin and Vegetable Society, the Bonsai Society of Victoria, the Bromeliad Society of Victoria, the Cacti and Succulent Society of Australia, the Chrysanthemum Society of Victoria, the North West and Early Morn African Violet Groups, the Fern Society of Victoria, the Pelargonium and Geranium Society of Victoria, various branches of the Society for Growing Australian Plants and the Victorian Carnivorous Plant Society.

Formal training in horticulture became available in the 1890s. In 1860 the HSV was granted 25 acres (10 ha) of a government survey paddock at Richmond augmented in 1862 with part of Richmond Park. The official opening of the Burnley Gardens on this site was the occasion for a flower show in 1863. But in 1891 escalating costs and bank crashes forced the Society to hand over the gardens to the government which established the Burnley School of Horticulture (later the Victorian College of Agriculture and Horticulture, Burnley campus and now part of the University of Melbourne's Institute of Land and Food Resources). Horticultural training is also offered at the Northern Melbourne Institute of TAFE, which includes the Northcote Nursery, and Holmesglen Institute of TAFE, which took over the former Victorian Schools Nursery in Glen Waverley.

A number of institutes devoted wholly or partly to horticultural research have been established. In 1909 the Department of Agriculture founded an experimental farm at Cheltenham. The Biology Branch of the Department of Agriculture was established at Burnley in 1929. Renamed the Victorian Plant Research Institute in 1965, and the Plant Research Institute in 1976, it conducted research into diseases and insect pests and provided a diagnostic and advisory service, as well as producing pathogen tested planting material. A Plant Quarantine Service was also located at Burnley. In 1993 the Institute's research activities were transferred to the Horticultural Research Institute at Knoxfield, established in 1950 as the Scoresby Horticultural Research Station to undertake research into fruits and ornamentals. This became part of the Institute of Horticultural Development (IHD) in combination with centres at Ovens and Toolangi. By 2003 the site at Knoxfield had been renamed the Knoxfield Centre, and the Toolangi and Ovens sites had been renamed the Toolangi Centre and the Myrtleford Centre respectively. These centres, with the Mildura Centre (formerly Sunraysia Horticultural Centre), are run by the Department of Primary Industry. The Keith Turnbull Research Institute, devoted to research on weeds and animal pests, was established in 1967 at Frankston (now the Frankston Centre). The Institute of Land and Food Resources is also involved in horticultural research.

Esther Anderson