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• Cold hardy rye genotypes accumulated the highest amounts and diversity of anthocyanins. • Glycosylated cyanidins were preferentially accumulated in cold hardy genotypes. • Delphinidin and pelargonidin glycosides were unrelated to cold hardiness. • A higher accumulation of anthocyanins in leaves than in crowns upon cold acclimation. Fall-seeded rye improve their frost resistance during a cold acclimation period in the fall, which is often associated with an accumulation of red/purple-colored anthocyanins in plant tissues. The pigments provide antioxidant activity and are proposed to scavenge excess reactive oxygen species (ROS) and mitigate light stress occurring during cold exposure. The relationship between anthocyanin and winter hardiness in rye (Secale cereale L.) was assessed by analyzing 96 genotypes with varying levels of winter survival. HPLC-QTOF MS/MS analyses of tissue extracts prepared from cold-acclimated plants revealed presence of accumulated anthocyanins in leaves of 74 genotypes and 51 of these showed low levels of anthocyanins presence in crown tissues. An overall higher abundance and diversity of anthocyanins was noted for the most cold-hardy as compared to the less hardy genotypes. A total of 18 anthocyanins originating from the pelargonidin, cyanidin, and delphinidin precursors were identified, of which the glycosylated cyanidins were accumulated in 37 of the 39 most winter hardy genotypes, but only detected in six of the 38 most tender genotypes. The link between anthocyanin concentration and profiles with winter-hardiness levels for the 96 rye genotypes suggested a role for cyanidin-derived anthocyanins in mediating enhanced winter hardiness in rye. [ABSTRACT FROM AUTHOR]