Phosphorylation is the most important post-translational modification in eukaryotes. Although many computational phosphorylation site prediction tools exist for mammals, and a few were created specifically for Arabidopsis thaliana, none are currently available for other plants.In this article, we propose a novel random forest-based method called PHOSFER (PHOsphorylation Site FindER) for applying phosphorylation data from other organisms to enhance the accuracy of predictions in a target organism. As a test case, PHOSFER is applied to phosphorylation sites in soybean, and we show that it more accurately predicts soybean sites than both the existing Arabidopsis-specific predictors, and a simpler machine-learning scheme that uses only known phosphorylation sites and non-phosphorylation sites from soybean. In addition to soybean, PHOSFER will be extended to other organisms in the near future.