Monitoring of the seed quality at different stages of plant breeding at sunflower represents a very important element in obtaining high yield hybrids based on CMS-Rf genetic system. Sunflower represents a protandric plant with a single terminal inflorescence which contains 700-3000 individual hermaphrodite flowers, exposed on the calathidium, making manual emasculation almost impossible. That’s why the utilization of the male sterility was indispensable and necessary for the obtaining of the high level of hybridization at all the stages of sunflower breeding. Wide utilization of maternal lines, with cytoplasmic male sterility, and of paternal lines, with fertility restoring genes Rf, lead to the necessity to observe the stability and homogeneity of parental genotypes. Thus, for the paternal genotypes it is important to verify the presence and the stare of Rf genes, but maintaining male sterility is verified by the level of sterility control. Utilization of PCR-based methods with specific primers allows controlling genotype quality.