In response to the challenge from phages, bacteria evolve a number of defense systems against phage invasion. Meanwhile, the phages evolve multiple counter-defense mechanism as well under the selection pressure from bacteria. The evolution relationship between bacteria and phages, as well as the functional mechanism, still remains to be uncovered. A novel immune system, CRISPR-Cas system, has been found in bacteria and archaea recently. With deeply research of the function and mechanism of CRISPR-Cas system, the coevolution relationship between bacteria and phages is becoming clear. In this review, the mechanism of CRISPR-Cas system-mediated immunity in prokaryotes is introduced. In particular, the progress on the role of CRISPR in the coevolution of bacteria and phage is reviewed.