A total of seven Kudingcha genotypes from three plant species (Ilex kudingcha, Ilex cornuta, and Ligustrum robustum) with different geographic origins in China were investigated for their major phenolic compounds, individual and total phenolics contents, and in vitro antioxidant properties (ABTS, DPPH, FRAP, and OH assays). LC-PDA-APCI-MS analysis showed that Kudingcha genotypes from flex and Ligustrum had entirely different phenolic profiles. Major phenolics in Kudingcha genotypes from two flex species were mono- and dicaffeoylquinic acids, whereas those in a Kudingcha genotype from Ligustrum were phenylethanoid and monoterpenoid glycosides. All Kudingcha genotypes of flex exhibited significantly stronger antioxidant capacities than that of Ligustrum. Within six Ilex genotypes, great variation existed in their composition of individual phenolic compounds and their antioxidant properties. The comparative data and LC fingerprints obtained in this study may provide useful information for screening and breeding of better Kudingcha genotypes and also for their authentication and quality control.