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Rye (Secale cereale L.) cultivation has a long history in the Alpine region, where local ecotypes have been honed through generations of human selection. Despite the introduction of commercial varieties during the 20th century, traditional ecotypes are believed to persist in Valtellina, especially in the medium/upper valley (Teglio and Bormio). Our study aims to identify and preserve these local rye ecotypes by comparing them to commercial varieties. We examined 14 rye accessions through population genetic analyses (by using eight SSR makers), agronomic trials (germplasm characters, plant traits, and yields), and phytochemical analyses (total phenolic compound, flavonoids, and the radical scavenging activity). Two commercial varieties were used—one from Poland, previously genetically characterized (C_POL_P1; i.e., P1 ancestry), and one with an unknown origin. Additionally, we analyzed eleven accessions from Valtellina (medium and upper valley) and one from another alpine valley in South Tirol (Laimburg; LAI). Molecular markers analysis revealed the presence of two distinct genetic lineages: the first (P1) comprised all Teglio accessions and the commercial one from Poland, while the second (P2) grouped the two alpine accessions from Bormio (upper Valtellina) and South Tirol, along with a commercial one of uncertain origin. The clusters P2 exhibited significantly lower average values of the number of alleles (z = 2.03; p < 0.05), Shannon index (z = 2.35; p < 0.05), and expected heterozygosity (z = 1.97; p < 0.05) than in P1. Significant differences were observed in plant traits and agronomic performance between P1 and P2 accessions, with the latter displaying superior traits. For instance, the seed weight of germplasm was the highest in P2 (H(chi2) = 22.44; p < 0.001). Phytochemical analyses did not reveal a clear pattern between genetic lineages but identified some very well-performing Valtellina landraces in terms of scavenging activity. Characterizing these local rye varieties helps establish a short food supply chain to support Valtellina's mountain economy. The medium valley (P1) and upper valley (P2) varieties have the potential for agroecological valorization, benefiting local farmers. Phytochemical analyses identified better accessions within P1 and P2 for nutraceutical use and commercialization. Additionally, selecting and conserving resilient ecotypes can address future challenges from extreme climate conditions. [ABSTRACT FROM AUTHOR]