As the most abundant biological entities on earth, bacteriophages (phages) were considered as the antagonists of bacteria. With the rapid development of genomics and molecular biology technologies, a subtle and complex relationship between phages and their host bacteria has been uncovered. Prophage refers to an intracellular form of a bacteriophage, which is usually integrated into the hereditary material of the host. Prophage is ubiquitously distributed in bacterial genomes. It reproduces when the host does and can affect important biological properties of their bacterial hosts, such as virulence, biofilm formation and host immunity. Interestingly, prophages were also involved in regulating the lysogeny-lytic state by "monitoring" the quorum sensing of bacteria. Recently, anti-CRISPR proteins encoded by prophages were found, which attracts a lot of attention. In this review, we summarized the prediction, distribution, classification and functions of prophages to lay a foundation for further studying interactions between phages and bacteria.