The research goal include adaptation and implementation of some basically studies for crop breeding and sunflower seed control involving, which is one of basic agricultural crops in the Republic of Moldova. Prospective hybrids obtaining by crop plants improving involves the application of efficient techniques that provide the initial material assessment used in breeding programs, including the genetic polymorphism estimation, inbred lines homogeneity determination and F1 hybridization degree, etc. Our researches were directed to morphological and molecular features revealing and their utilization in hybrid vigor prognosation, both with selection of most prospective inbred lines. The genetic variability estimation was based, in this study, on seed morphological parameters evaluation (seed mass, core mass, shell mass, seed length and width), on protein polymorphism spectra analysis of helianthinin and PCR analyses using specific and SSR primers of nine F1 sunflower hybrids and their parental lines. Dispersional and correlational analyses implementation allow to display those morphological and molecular features which correlate with seed productivity, and associated with heterosis manifestation factors. The helianthinin electrophoretic analysis showed variability at the level of β chain polypeptides of C subunit (Mr 20-25 kDa) and at the level of stable dissociation component (58 şi 61 kDa), which were used for standard spectra elaboration for every studied genotype, its frequency characterizing the biological genotype purity. Also, were proposed the level estimation hybridization method based on SSR markers and the evaluation method of sterility level in CMS lines, both based on PCR technique. Despite different analyses of sunflower genotypes, cluster analysis based on genetic SSR similarity and Mahalanobis distance of morphological features produced similar dendrograms. It has been found that the specific seeds and plants peculiarities revealed by correlation analysis shows that the qualitative traits in combination with the Mahalanobis distance between parental genotypes are relevant indexes, which can be used to predict the heterosis effect.