Remote sensing of individual tree species has many applications in resource management, biodiversity assessment, and conservation. Airborne remote sensing using light detection and ranging (LiDAR) and hyperspectral sensors has been used extensively to extract biophysical traits of vegetation and to detect species. However, its application for individual tree mapping remains limited due to the technical challenges of precise coalignment of images acquired from different sensors and accurately delineating individual tree crowns (ITCs). In this study, we developed a generic workflow to map tree species at ITC level from hyperspectral imagery and LiDAR data using a combination of well established and recently developed techniques. The workflow uses a nonparametric image registration approach to coalign images, a multiclass normalized graph cut method for ITC delineation, robust principal component analysis for feature extraction, and support vector machine for species classification. This workflow allows us to automatically map tree species at both pixel- and ITC-level. Experimental tests of the technique were conducted using ground data collected from a fully mapped temperate woodland in the UK. The overall accuracy of pixel-level classification was 91%, while that of ITC-level classification was 61%. The test results demonstrate the effectiveness of the approach, and in particular the use of robust principal component analysis to prune the hyperspectral dataset and reveal subtle difference among species.