A search and a combination of different statistical methods for determining the similarity and difference between genotypes is a hot topic for breeding. In the formation of adaptive potential and appropriate protective mechanisms for the implementation of the adaptive potential of sugar beet, terpene compounds and saponins are involved. To determine polymorphism based on DNA of sugar beet materials under investigation, RAPD analysis was performed. A cluster analysis of the hybrids affinity was carried out in terms of the qualitative biochemical state of the system and DNA polymorphism. As a result, it was found that hybrids that demonstrated high activity of the secondary metabolism and, consequently, showed different ability to form a high adaptive potential in the conditions of long-term cultivation in vitro, formed separate clusters. With the aid of RAPD markers, the authors also determined two clusters that were formed on the basis of genotype affinity. In order to determine the correlations between genetic distances obtained by RAPD markers and terpene compounds, the Mantel test (linear correlation for Pearson) was performed. The values of coefficients r = 0.517 were obtained at α = 0.05. However, according to the data interpretation, the calculated value of p (0.088) was higher than the significance level of α = 0.05, which indicates the absence of correlations between the matrices under investigation. Thus, the revealed genotypic features of the secondary metabolism and genetic distances are additional characteristics for evaluation of the ecological plasticity of sugar beet plants, which is important in the breeding process.