Background. Polymorphism analysis was done for the core genome sequences of nodule bacteria of S. meliloti species in order to identify chromosomal types and to evaluate the occurrence of accessory elements (genomic islands) in them. Materials and methods. Chromosomal studied loci were: betBC (marker M-I) and SMc04407-SMc04881 (marker M-II) both are related to metabolic processes and stress tolerance, and 16S-23S intergenic sequences (marker M-III) to search phylogenetical distance at intraspecies level. Results. Significant differences between the occurrence of alleles of gene-markers M-I/M-II and MIII were determined between strains related to tested the 5 typical groups and 9 subgroups of strains differing by geographical region/source (nodule, soil) of isolation, as well as by salt tolerance. Four chromosomal types were identified among tested S. meliloti native isolates and a preference occurence of one of the three islands Rm1021 in links with particular chromosomal type was shown. The significant prevalence of strains with particular chromosomal type was shown for S. meliloti populations native to centers of alfalfa diversity at the NE of Caucasus, as well as at NE of Kazakhstan (Aral sea related region), as well as in agrocenoses. Conclusion. It was predicted that strains inherited altered markers M-I/M-II may belong to divergent clonal lines occured in both centers of alfalfa diversity, while strains with altered sequences of all three markers could be a representatives of a new S. meliloti biovar(s), the formation of which is occurred much more intensively at the modern center of the introgressive hybridization of alfalfa at NE of Kazakhstan.