In the studies of Melilotus dentatus Pers. populations from different geographically remote areas (North Caucasus and Kazakhstan), a compex approach of intra- and inter-population analysis of taxonomically important molecular markers (ITS) was used. The analysis of receptor gene nfr5 was also made. It is shown that the Melilotus dentatus Pers. plants differ at both intra- and inter-population levels. A consolidation of sweet clover's populations to clusters is observed according to their geographic location. An independent distribution of populations on receptor part of nfr5 gene concerning cluster structure of ITS region is determined.