Timely and accurate information about spatial distribution of tree species in urban areas provides crucial data for sustainable urban development, management and planning. Very high spatial resolution data collected by sensors onboard Unmanned Aerial Vehicles (UAV) systems provide rich data sources for mapping tree species. This paper proposes a method of tree species mapping from UAV images over urban areas using similarity in tree-crown object histograms and a simple thresholding method. Tree-crown objects are first extracted and used as processing units in subsequent steps. Tree-crown object histograms of multiple features, i.e., spectral and height related features, are generated to quantify within-object variability. A specific tree species is extracted by comparing similarity in histogram between a target tree-crown object and reference objects. The proposed method is evaluated in mapping four different tree species using UAV multispectral ortho-images and derived Digital Surface Model (DSM) data collected in Shanghai urban area, by comparing with an existing method. The results demonstrate that the proposed method outperforms the comparative method for all four tree species, with improvements of 0.61–5.81% in overall accuracy. The proposed method provides a simple and effective way of mapping tree species over urban area.