Alternate bearing in citrus trees has been extensively studied as a key feature for citrus growers. Although the genetic and the biochemical process occurring during alternate bearing has been studied extensively, there is a lack of information identifying the presence of metabolic indicators during ?on? and ?off? years. In citrus plants, leaves play a central role in the metabolic pathway triggering the flowering induction process. To investigate the changes during this transition, a liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) analysis of the leaf profiles of 20 compounds (17 polyphenols, two limonoids, and one furanocoumarin), in bearing and non-bearing branches arising from four different mandarin genotypes, was performed. The same metabolites were found in all the genotypes at both stages: both limonoids and 11 polyphenols. Using these compounds, the chemotaxonomic differentiation between cultivars was assessed. The levels of flavanones and limonoids showed differences in both bearing stages and the transition from vegetative to flowering could be shown by the activation of the polyphenol biosynthetic pathway, from precursors like naringenin to metabolic end-points such as narirutin and polymethoxyflavones. Narirutin levels showed significant differences between both stages, suggesting it as a possible marker of the physiological status of the branch. View Full-Text