The berries from the native Chilean Gaultheria phillyreifolia and G. poeppigii are appreciated for their sweet taste and aroma. Fruits from both species were investigated for their secondary metabolite composition and antioxidant activity. The extracts were submitted to membrane chromatography to separate anthocyanins from copigments. Four anthocyanins were isolated by counter-current chromatography (CCC) and identified as cyanidin galactoside, cyanidin arabinoside, delphinidin galactoside and delphinidin arabinoside. From the copigments, CCC allowed the separation of quercetin(Q)-3-arabinoside, Q-3-rutinoside Q-3-rhamnoside and 3-caffeoylquinic acid. Additionally, the iridoids monotropein-10-trans-coumarate, monotropein-10-trans-cinnamate and 6α-hydroxy-dihydromonotropein-10-trans-cinnamate were isolated. The latter two iridoids are reported here for the first time. Some 34 other compounds were tentatively identified by HPLC-DAD-ESI-MSn. The antioxidant activity showed differences between anthocyanins and copigments from both species. Main compounds were quantified and submitted to a Partial-Least Square Discriminant Analysis (PLS-DA). This is the first report on the isolation of phytochemicals from the selected Chilean Gaultheria species.