The polyphenolic composition of two Fortunella margarita (Nagami kumquat) specimens from Greece and Egypt was investigated employing fractionation by solvent partition and liquid chromatography-mass spectrometry. The main groups of phenolics identified in the different fractions generated were C-glycosylated flavones, O-glycosylated flavones, C-glycosylated flavanones, O-glycosylated flavanones, flavonols, chalcones, phenolic acids and derivatives thereof. The antioxidant potency of the fractions was assessed using two representative in vitro tests, including antiradical activity and hydroxyl free radical scavenging activity. It was revealed that the ethyl acetate fractions from both specimens contained the higher polyphenol content and exhibited the better antioxidant characteristics. The results indicated that F. margarita peels may be regarded as a rich source of potentially bioactive polyphenols.