Leaf shape analysis of three Aquilaria species was undertaken using Elliptical Fourier descriptors (EFD) within a research planting in tropical Australia. This approach was taken to develop a method for discriminating the species in the absence of reproductive traits or genetic analysis and as a morphological scale of leaf variation. Leaf outlines were analysed to distinguish variability between species. Principal components analysis and canonical discriminant analysis were applied to group the species based on 25 Fourier descriptors. Four components were required to explain 78 % of the variance and the first and second canonical functions discriminated three groups of species therefore EFD was a useful approach for analysing leaf outline variability and distinguish species in the genus Aquilaria. This approach provides a rapid method that could assist in the species identification in Aquilaria where reproductive traits are absent.