In the present study, thirteen SSRs (Simple Sequence Repeats) were employed for screening the level of similarity between sunflower parental lines and progeny obtained in final stages of selection. Another aim of the study was to compare the success of making isogenic lines through selection. Line P (donor line) was used as a donor of downy mildew gene Pl 6 and backcrossed with four commercial inbred lines (A, B, C and D) susceptible to downy mildew. HAP3, a DNA-specific primer, was used to test the success of transfer of P l6 gene from the donor line to the progeny lines in the Pl 6 and Pl 7 generations. It was found that all progeny lines were resistant to downy mildew. Results obtained by using thirteen primers showed that progeny lines were similar to their respective recipient parent, but further studies have to be conducted using a larger number of primers and a larger number of genotypes.