Clear-cut identification of elite crop varieties and hybrids is essential for guarantying purity of hybrid seeds. Unwanted self-pollination in field or during crossing programs is one of the major sources of impurity of hybrid seeds that interferes with trait improvement via conventional breeding programs or variety improvement via backcross scheme. Conventional characterization of hybrid seeds based on specific morphological and agronomic data is time-consuming, restricted to a few characteristics, and is influenced by environment. In contrast, DNA-based markers are highly heritable, available in high numbers, and exhibit enough polymorphism; hence they can be used to trace the alleles came from a given parent. To estimate the interference rate of self-pollination with the variety improvement, hybrid seeds in several backcross generations were studied using SSR markers. Results showed that in the case of hybrid seeds produced under uncontrolled low-stringent conditions frequency of off-types seeds ranged from ~17% (for BC1 of cross Sadri x Neda) to as high as 50% (for BC3 of cross Sadri x Neda) and averaged up to 40%, that may be seem an unexpected value. However, in the case of hybrid seeds produced under completely controlled conditions any off-type seeds were not found. Thus, we suggest that make crosses under completely controlled conditions to guarantee the production of true hybrid seeds.