The genetic structure of 19 accessions of Salvia officinalis from the genebank Gatersleben (Germany) was analyzed with SNP and SSR markers developed from EST sequences of Salvia fruticosa. Analyzes were performed exclusively with HRM (high resolution melt analysis), the alleles were identified applying a beforehand developed strategy for codominant markers. Nine polymorphic markers (PIC between 0.12 and 0.61) were used for a complete allele scan in the sample set of 190 individuals from 19 accessions. AMOVA stated 51% of variance between the populations and 49% within. Principal component analysis showed a main bulk of closely related accessions, which have substantial heterogeneity within themselves. However, some populations, especially two from Romania, were clearly distant. This is in accordance to phytochemical results of the same sample set, where the Romanian populations were distant due to an exotic chemotype of the essential oil. Cluster analysis revealed connections between groups of accessions in detail. (C) 2010 Elsevier Ltd. All rights reserved.