DNA markers usefulness in breeding strategies has been limited by technical considerations. The plant breeding programs effectiveness has increased considerably due to selection through molecular markers. Over phenotypic markers used as standard by breeders, molecular markers have a great advantages because it reveal genetic variability, not influenced by environmental activity and facilitates their use in genetic and phylogenetic analyzes. The random amplified polymorphic DNA (RAPD) fingerprinting method is random DNA fragments amplification carried out by PCR, using of arbitrary nucleotide single primers sequence that is simple, less expensive and have rapid ability of extensive polymorphism DNA detecting. The RAPD-PCR analysis can provide the essential information for genetic sampling development, germplasm study, conservation and breeding assisted by molecular markers. In this paper RAPD-PCR technology by 45 primers was used to analyze the genetic structure of six different plant species: crops (Helianthus annuuus, Cucumis sativus) and medicinal and aromatic plants (Mentha spicata, Salvia sclarea, Hypericum perforatum and Origanum vulgare). The results obtained showed different levels of inter- and intraspecific variability and the RAPD primers efficacy in genetic structure analysis of various plant species. Thus, among the tested primers, 32 proved useful results of amplification to characterize these species, 13 primers - amplified genotypes of one species and 19 - amplified the genotypes in two or three of the species included in the study. Whereas 13 primers were excluded due to the absence of amplification or to the amplification of the same single fragment in all samples. The highest molecular polymorphism has been revealed to RAPD-PCR analysis with eight primers (OPA2, OPA9, OPB10, OPG5, OPK17, OPH15, P37, P28). Five of them (OPA2, OPA9, OPB10, OPG5, OPK17) highlighted significant genetic variability at S. sclarea, H. perforatum and O. vulgare. Primer OPH15 showed activity in S. sclarea, O. vulgare and H. annuuus plant species. P37 are specific for H. annuus, C. sativus and M. spicata. RAPD primers P36, P44, P48, P49 showed an amplification products yield on 2 species of plants (C. sativus and M. spicata) and OLIGO-A1, OLIGO-A2, UBC215, UBC250 RAPD primers have been highlighted on S. sclarea and O. vulgare. The most informative RAPD primer with a maximum number of amplified bands and emphasized polymorphism at S. sclarea was UBC250, at H. perforatum OPA9, at O. vulgare - UBC215, at M. spicata P37, at C. sativus - P28, P44 and P2 at H. annuus respectively. Generalizing the obtained data can conclude that genetic analyzes with RAPD markers highlighted the genetic high heterogeneity, shows high variability of breeding material by number of sites, size and content.