Abstract: For plague surveillance in the silence periods, the whole genome sequences of 10 Yersinia pestis strains and 3 Yersinia pseudotuberculosis strains downloaded from Internet were compared. In the 68 Y. pestis Tectonics divided according to CO92 chromosome sequence, 67 appeared in Y. paeudotuberculosis genomes in whole or in most part, the arrangement of these tectonics were determined. Y. pseudotuberculosis has the same 7 copies of rRNA gene clusters as Y. pestis, and they caused the earliest genome rearrangement in Y. pseudotuberculosis. Before Y. pestis evolved from Y. pseudotuberculosis, there were 16 positions inserted with 4 species of insertion sequences, and no rearrangement caused by these insertion sequences was found in Y. pseudotuberculosis. Totally 20 Pestis-Islands (PeI) specifying for Y. pestis and 39 Pseudo-Islands (PsI) specifying for Y. pseudotuberculosis were identified, and their sequences could be used as differentiation characters when atypical strains appeared in the surveillance.