Citrumelo CPB 4475 and Carrizo citrange are two citrus genotypes that differ in their tolerance to abiotic stress. Little information is found on flavonoid content in citrus leaves and even less on the role of flavonoids on citrus tolerance to environmental stress. This work developed a multiplexed approach utilizing HPLC-DAD-ESI-MS and NMR for the identification and profiling of flavonoids in citrus leaves. A total of 47 phenolic compounds were detected and 45 tentatively identified. Eleven of them were acylated with hydroxycinnamic acid derivatives. Some of the compounds identified were not reported in citrus and two of them not even in the plant kingdom. In response to soil flooding, the relative reduction in leaf flavonoids was more important in citrumelo, which can give additional insights to the low tolerance of this genotype to flooding. The method reported could serve as an effective tool for profiling flavonoids in leaves of different genotypes under distinct environmental situations.