Publicly supported collections of cultivated germplasm are one of the key sources of new genes for crop improvement. VNIIMK is the leading organization in oil and essential oil crop breeding and seed growing in the Russian Federation with more than a century-long history. Sunflower varieties created by V.S. Pustovoit at VNIIMK became the basis for the development of the modern sunflower varieties worldwide. In the present study 186 sunflower lines from the VNIIMK collection were characterized based on their genotype and general morphological and phenological economically-important traits. Additionally for 99 sunflower lines fatty acid content seed oil content seed husk content 100-seed weight and seed number in the head were determined. Sequencing of RAD-libraries and the subsequent analysis have identified 65553 variants including SNPs and indels. LD analysis revealed substantial variability across the genome. The longest LD blocks (>5000 Kb) were found in the linkage groups 1 5 and 17. The analysis revealed significant genetic and phenotypic diversity of the VNIIMK sunflower collection. Novel significant associations with linolenic acid content in the seeds were found on LGs 8 9 and 17.