Partial nucleotide sequence of 16S rRNA (16-989 nn.) of plague agent (Yersinia pestis) was determined after sequencing of cloned cDNA fragments. The comparison of Y. pestis 16S rRNA sequence with that of E. coli shows a number of point sequence variation due to base changes. The base changes are found in 16S rRNA secondary structure regions that are localized on the surface of 30S ribosome subunit (hairpins 6 and 18) as well as in the regions that bind the proteins S8, S15, S16 and S20. These proteins of Y. pestis differ from the same proteins of E. coli by electrophoretic mobility, when analyzed by two-dimensional co-electrophoresis in polyacrylamide gel. The correlation between the structure of the four proteins and the structure of their binding sites in 16S rRNA are discussed.