Huanglongbing (HLB) is the most destructive disease of citrus worldwide. The disease is caused by the proto-bacteria Candidatus Liberibacter asiaticus and transmitted by the Asian citrus psyllid Diaphorina citri. HLB symptoms are slow to appear, while the tree continues to be a source of inoculum. Monitoring tree health and rapid detection of HLB is critical for sustainable citrus production. Nowadays, scientists are working on developing new techniques for pre-symptomatic detection of HLB, as there is no available method for real-time assessment of tree health. In this study, we demonstrate the rapid and efficient discrimination between healthy and HLB-affected of citrus by laser-induced breakdown spectroscopy (LIBS) combined with chemometric analysis. Healthy and HLB-affected trees were differentiated with a high degree of precision. The novelty of this method lies in the fingerprinting of healthy and diseased plants based on their organic and inorganic constituents, and the use of a multi-pulse laser coupled with a microscope to take spectra of the plant phloem.