SSAP method was used to study the genetic diversity of 22Linumspecies from sectionsLinum,Adenolinum, Dasylinum, Stellerolinum, and 46 flax cultivars. All the studied flax varieties were distinguished using SSAP for retrotransposonsFL9andFL11. Thus, the validity of SSAP method was demonstrated for flax marking, identification of accessions in genebank collections, and control during propagation of flax varieties. Polymorphism ofFl1a, Fl1b, andCassandrainsertions were very low in flax varieties, but these retrotransposons were successfully used for the investigation ofLinumspecies. Species clusterization based on SSAP markers was in concordance with their taxonomic division into sectionsDasylinum, Stellerolinum, Adenolinum, andLinum. All species of sect.Adenolinumclustered apart from species of sect.Linum. The data confirmed the accuracy of the separation in these sections. Members of sectionLinumare not as closely related as members of other sections, so taxonomic revision of this section is desirable.L. usitatissimumaccessions genetically distant from modern flax cultivars were revealed in our work. These accessions are of utmost interest for flax breeding and introduction of new useful traits into flax cultivars. The chromosome localization ofCassandraretrotransposon inLinumspecies was determined.