Citrus plants are one of the most economical fruit bearing trees grown worldwide for their medicinal use as well as for the flavor and food industry. This study attempts to characterize the metabolome difference in polyphenols of four Citrus species fruit peels; C. reticulata Blanco cv. Egyptian, C. sinensis (L.) Osbeck cv. Olinda Valencia, C. aurantiifolia Swingle cv. Mexican and C. paradisi Macfad. cv. Duncan via ultra-performance liquid chromatography coupled with quadrupole-time-of-flight-mass spectrometry platform. A total of 163 metabolites were characterized of which 28 were detected for the first time in Citrus cultivars including eight coumarin derivatives, three cinnamic acids conjugates, one polymethoxyflavone, 5 O-glycosides, 2 C-glycosides, three flavone-di-O-glucosides and six acetyl sugar derivatives of luteolin and kaempferol in addition to oxygenated and methylated fatty acids. Flavonoids amounted for the most abundant secondary metabolites class in the studied Citrus peels. The relative variability among these Citrus peels was estimated using clustering analysis with flavonoids accounting for cvs. segregation. Hierarchical clustering analysis revealed the chemical similarity of C. reticulata, C. sinensis and C. paradise peels and being distant them from that of C. aurantiifolia. To the best of our knowledge, this study provides the first report for metabolite compositional differences in these four Citrus peels.