Abstract: Objective Protein coding sequences in the origin tectonics in Yersinia pestis genome were annotated according to the existence of the ribosome binding sites. Methods Select a characteristic plate in Y.pestis, count the quantity of CDS with tranditional and RBS methods, compare their consistency. Find the location of mutations and their affect on the CDS by blast 10 Y.pestis, determine the reliability of the RBS methods. Results In the annotation of the CO92 sequence, 47 CDS existed in this section. By the method in this research, 74 CDS could be identified, 24 were completely identical to the original annotation, and 8 were partially identical. Nine CDS were found to have multiple starting codons. Most of the 42 new discovered CDS encoded short peptides less than 100 amino acids. The influence of mutation to the CDS was checked in 10 strains of Yersinia pestis. In this section of genome, 36 mutation loci were identified. According to the original CO92 annotation, 12 CDS were influenced, but according to the RBS annotation, the influenced CDS decreased to 9, and other 3 reduced the lethality. Conclusion The result of the research suggested that RBS could be the most important index in the CDS annotation, but could not be used to replace the method based on the Markove model at present.