Metabolic profiling of cactus samples collected on Jeju Island (Opuntia ficus-indica) and in Sinan, Jeonnam province (O. humifusa) was carried out using high performance liquid chromatography-electrospray ionization mass spectroscopy (HPLC-ESI-MS) and multivariate statistical analysis. The samples were classified into two characteristic groups and the flavonoid glycosides accounting for the observed variations were identified by MS/MS analysis. This approach provided an overview of the differences among plant products originating from differences in the genetic nature of plants.