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This study provided a detailed profiling of the antioxidant and bioactive compounds occurring in three varieties of <i>Rubus idaeus</i> L. fruits (“Fall Gold”, “Glen Ample” and “Tulameen”) compared to <i>Rubus occidentalis</i> L. black raspberry (“Jewel” cultivar), adopting a comprehensive untargeted metabolomics approach developed with UHPLC analysis coupled with quadrupole/time-of-flight high resolution mass spectrometry, using the SWATH^® acquisition protocol. The feature selection and annotation workflow, applied to the analysis of raspberry extracts in both polarities, allowed identifying 68 bioactive compounds mainly belonging to the classes of (poly)phenolic compounds. Interestingly, some of these identifications (e.g., ferulic acid glycosides and the ellagitannin-like nobotanin/malabathrin) represent the first report in raspberry fruits. Principal component analysis made possible highlighting the features more related to the expression of a genotype effect within the <i>R. idaeus</i> species or between the two raspberry species herein investigated. Overall, flavanols were the most discriminating features for the Fall Gold variety, whereas ellagitannins and flavonol glycosides represent more distinctive metabolic traits in Glen Ample and Tulameen fruits. Moreover, <i>R. occidentalis</i> Jewel variety was strongly characterized by the occurrence of anthocyanins, such as cyanidin, pelargonidin and delphinidin glycosides.