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Simple Summary Aggressive-invasive species often interact with native ones, thus considerably changing the biological communities, with ecological, economic, and even social effects. It is a challenge to evaluate the direction and the rate of microevolution in native and introduced populations. One of the ways to do this is to estimate the genetic diversity. An introduction often imposes a reduction in population size (genetic drift, bottleneck, founder effect), which has the potential to reduce genetic diversity. However, after a lag, the genetic diversity can be restored due to repeated invasions (multiply introductions), hybridization between individuals from two different subspecies or species in the invaded ranges, as well as during rapid genetic changes under selection pressures in the novel environment. The purpose of this study was to determine the level of genetic diversity in successful invasive species Lupinus polyphyllus Lindl. and Heracleum sosnowskyi Manden. from Russia and Ukraine, and whether it may be associated with the strategy of their further expansion. Abstract In our study, two aggressive-invasive species, Lupinus polyphyllus Lindl. and Heracleum sosnowskyi Manden. from Russia and Ukraine, were investigated. The success in naturalization of both species is associated with human activities, since they have been used in agriculture and floriculture and both have qualities such as environmental tolerance, high fertility and phenotypic plasticity. The purpose of this study was to determine the level of genetic diversity of both species. For Heracleum sosnowskyi Manden., genetic diversity was compared in invasive and native populations. For Lupinus polyphyllus Lindl., the genetic diversity was compared in variety, feral and invasive populations. A genetic diversity was formulated using RAPD, ISSR and REMAP. For Heracleum sosnowskyi Manden., the average genetic diversity within the invasive population was similar (0.432), but slightly less (0.502) than within the native Caucasian population. This may suggest the successful naturalization of invaders and almost complete reconstruction of their genetic diversity. For Lupinus polyphyllus Lindl., the genetic diversity for the invasive population was the highest, with an average of 0.294, while for variety, it was the lowest, with an average of 0.194. The feral population had an intermediate place with an average of 0.248, which could suggest an increase of diversity in the process of naturalization.