Clustered regularly interspaced short palindromic repeats（CRISPR） are the genetic structures existing in most bacteria and archaea. They can effectively prevent the invasion of exogenous DNA （plasmids， phages， etc.）， and then prevent the horizontal transfer of foreign genes. Object： Shigella boydii， Shigella dysenteriae， Shigella flexneri and Shigella flexneri which are common in Shigella spp. 40 strains were studied to explore the structural differences of CRISPR loci and the relationship between CRIPSR and the plasmid in different species. Method： The bioinformatics methods were used to compare the homology of spacers and insert sequences and the relationship between the CRISPR locus and RNA secondary structure stability. Result： The results showed that there were CRISPR structures in all 40 Shigella strains， including 241 CRISPR loci and 6 loci. Repeat sequence and cas3 gene can not be used as a classification basis for these four types of bacteria. Conclusion： Although we found there was no statistical relationship between the number of CRISPR loci and the number of spacers， the original genetic motifs of spacer sequence integron and drug resistance gene had some homology， indicating that Shigella in the evolutionary process in the constant invasion by exogenous genes.