Abstract: Objective To understand the regularity of spacer sequences in clustered regularly interspaced short palindromic repeats (CRISPR) distributed in prokaryotes to which the complete genome sequencing was completed, and find the spacer sequences originated from bacteriophages. Methods From CRISPR database, 90096 spacer sequences identified from bacterial genome sequences were obtained and 1444 bacteriophage sequences from GenBank were used to establish the database. All the spacer sequences were aligned by using bacteriophage database with BLASTN software. Enumeration data were analyzed with 2 test. Results Among 2762 genomes, there were 1940 genomes with CRISPR or with possible CRISPR and 90096 spacer sequences in these CRISPR. Most genome had 1~50 spacers (1414/1940, 72.9%). Only 58 genomes had 250 spacers (58/1940, 3.0%). Among these genomes, 13 were from archaebacteria and the other 45 genomes were from true bacteria, the difference was statistical significant (2=29.98,P 0.01). The 1055 spacer sequences form 245 bacteria strains completely matched to 363 bacteriophages sequences, the rate was only 0.12%. Conclusion The number of spacer sequences in CRISPR differed among prokaryote genomes. There were more spacer sequences in CRISPR of archaebacteria genomes than in those of true bacteria genomes. The rate of spacer sequence originated from bacteriophages was low, which was related with the less detection of bacteria and bacteriophages genomes. Further research can improve the effective discovery.