Paenibacillus larvae is the etiological agent of American Foulbrood disease (AFB), a highly contagious and worldwide spread bacterial disease that affects honeybee brood. In this study, all fourteen complete P. larvae genomes available on the NCBI database were analysed for the presence of prophages using the PHAge Search Tool Enhanced Release (PHASTER) software. A total of 55 intact prophages were investigated for the presence of virulence, antibiotic resistance or other genes that might confer advantages to their bacterial hosts. This will provide improved knowledge on the impact of prophages in the evolution of bacteria, either by discovering new features assigned by prophages or by assessing the impact of foreign DNA in the interruption of host genes. Our data shows that 11 out of 14 P. larvae genomes have intact prophages, 3.9 ± 2.9 per genome in average. Genomic analysis indicate that all the prophages may be classified as Siphoviridae or Myoviridae. Around 60% of them have the attachment sites (attL/attR) located in intergenic regions, while the remaining 40% have them in the middle of genes, being the gene ImmA/IrrE (family metallo-endopeptidase) preferentially interrupted. We detected at least nine different integration zones in P. larvae genomes where a total of 21 prophages can be integrated. A closer look at prophage genomes revealed several genes responsible for the improvement of host performance, such as metabolic and antimicrobial resistance genes, toxins or bacteriocins. This demonstrates that the prophages harboured by P. larvae may influence their virulence and fitness capacities.