Rye stem rust (caused by Puccinia graminis f. sp. secalis, Pgs) causes considerable yield losses in rye crops grown in continental climates. In Germany, stem rust resistance in rye has attracted little attention until now. In order to implement resistance breeding, it is of utmost importance to (1) analyze Pgs populations in terms of diversity and pathotype distribution, and (2) identify resistance sources in winter rye populations. Within a three-year research project, we analyzed 389 single-pustule-isolates, collected mainly from German rye-growing areas, on 15 rye inbred differentials with different avirulence/virulence patterns; among them, 226 pathotypes were identified and only 56 occurred more than once. The majority of isolates infected 5-6 differentials. This high diversity was confirmed by a Simpson index of 0.99, a high Shannon index (5.27) and an evenness index of 0.97. In parallel, we investigated stem-rust resistance among and within 122 genetically heterogeneous rye populations originating from 19 countries across 3 to 15 environments (location-year combinations) in two replicates. While 7 German commercial rye populations were highly susceptible, 11 non-adapted populations, mainly from Russia, Austria and the USA, were highly resistant, harboring 32-70% resistant stems on plots averaged across 8 to 10 environments. Selections for low disease severity at the adult-plant stage in the field also displayed resistance in leaf-segment tests (r=0.86, P<0.01). In conclusion, rye stem rust pathogen populations are highly diverse and the majority of resistances in rye populations are race-specific. The new Pgs isolate set firstly developed within the project covers the current spectrum of virulences and can be used to assess the effectiveness of stem rust resistance genes or sources. New pathotypes can be detected using this differential set and farmers and industry can be alerted to circumvent economic damage. In the long term, resistances from non-adapted populations should be introgressed into commercial rye cultivars.