BackgroundPhages play a pivotal role in the evolution of microbial populations. The interactions between phages and their hosts are complex and may vary in response to host physiology and environmental conditions. Here, we have selected the genomes of some representativeBacillusprophages and lysosomes from the NCBI database for evolutionary analysis. We explored their evolutionary relationships and analyzed the protein information encoded by hundreds ofBacillusphages.ResultsWe obtained the following conclusions: First,Bacillusphages carried some known functional gene fragments and a large number of unknown functional gene fragments, which might have an important impact onBacilluspopulations, such as the formation of spores and biofilms and the transmission of virulence factors. Secondly, theBacillusphage genome showed diversity, with a clear genome boundary betweenBacillusprophages andBacilluslytic phages. Furthermore, genetic mutations, sequence losses, duplications, and host-switching have occurred during the evolution of theBacillusphage, resulting in low genome similarity between theBacillusphages. Finally, the lysis module played an important influence on the process ofBacillusphage cross-species infestation.ConclusionsThis study systematically described their protein function, diversity, and genome evolution, and the results of this study provide a basis for evolutionary diversity, horizontal gene transfer and co-evolution with the host inBacillusphages.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12866-023-02907-9.