The trees are without doubt the highlight of this garden. There are several hundred trees in total, with many of them at the height of their maturity. Trees of seventeen species in the gardens are currently listed by the National Trust of Australia, of which three are of State significance: the rare Chilean Wine Palm (Jubaea chilensis), seldom found in such a cool climate; the Variegated Portuguese Laurel (Prunus lusitanica 'variegata'); and a Coastal Live Oak (Quercus agrifolia). There are at least 13 species or varieties of oak (Quercus), 10 of elm (Ulmus), 8 of ash (Fraxinus), and 7 of hawthorn (Crataegus). Like may Victorian gardens, there are a great many conifers, including multiple specimens of cedar (Atlas, Blue Atlas and Deodar), redwood, big tree, Douglas Fir, six types of pine, nine different cypresses and representatives of several other species. There are several specimens of Himalayan White Pine (Pinus wallachiana), now uncommon in cultivation, and the only known examples of live oak (Quercus virginiana) and White Ash (Fraxinus americana) outside of the Royal Botanic Gardens, Melbourne. Many trees in the north-eastern sector of the gardens are labelled.

Several of the trees were planted to commemorate events, including an English Oak (Quercus robur) on one of the jubilees of Queen Victoria; an Algerian Oak (Quercus canariensis) for the marriage of Edward, Prince of Wales and Alexandra, planted on 19 May 1863 and named the Queen's tree in honour of Queen Victoria (an ash and a pine were also planted on that day ); an English Oak on the coronation of Edward VII and Alexandra in 1902; an Algerian Oak on the birthday of Princess Elizabeth on 23 June 1947; a silver maple (Acer saccharinum) planted in 1986 to commemorate the 150th anniversary of the State of Victoria; an oak (Quercus dentata) on 8 September 1988 for the bicentenary of Australia; and a golden red oak (Quercus rubra aurea) in 1990 for the 125th anniversary of the Shire of Kyneton (died, then replaced in 2007).

Click here to view a map of the locations of the most significant trees, or view a list of trees mentioned in 1872 and of those present in 1985.