Gillies Hill hosts a large array of plants native to Central Scotland. The hill is home to at least 38 Ancient Woodland indicator species from the AWVP - Europe/National/Scotland list and 21 from the AWVP - Scotland list, a record Scots Pine, a record Rowan, and an abundance of wildflower, lichen, fungi, moss, and grass species. Eight of the top ten Scottish plants listed on the Scottish Biodiversity List (a list of flora, fauna and habitats considered by Scottish Ministers to be of principal importance for biodiversity) as most popular among Scots can be found on Gillies Hill: common and bell heather, Scottish bluebell or harebell, Scots Pine, oak, thistle, rowan, ferns, and common spotted and Northern marsh orchids. Three of these including the heather, harebell, and Scots Pine are predominantly found on the hill's heath out-crops which are threatened by quarry expansion, as is the only known population of blaeberry on the hill.