Most host-associated viruses are bacteriophages (phages), which infect bacteria rather than eukaryotic organisms. Early research indicates that phages may play a role in regulating a host’s gut microbiome, which in turn may impact host health. Phages have two types of lifestyles: lytic and lysogenic. Lytic phages immediately replicate within and destroy bacteria, while lysogenic phages integrate into bacterial DNA and form a prophage, which replicates with the bacteria until environmental triggers induce lysis. Prophages can also encode useful toxins or metabolic genes within bacteria. The complexity of most animal microbiomes can make bacteria-prophage interactions difficult to study. However, the European honey bee (Apis mellifera) has a relatively limited and well-characterized set of core gut bacteria. Approximately 200 genomes (fragmented and complete) from honey bee gut-associated bacteria are published on NCBI, representing isolates from all nine major phylotypes and two bacterial pathogens. We conducted an initial survey of prophages in the honey bee gut by analyzing these 200 genomes through two different phage hunting tools: ViralRecall and PHASTER. High confidence phage candidates were identified. Our initial results indicate that the number of prophages within an individual genome varies between bacterial genera, with an approximate range of 0 – 9 phage regions per genome. Prophage per genome was highest among the pathogen Paenibacillus larvae (causative agent of American foulbrood) and in the core microbiota Snodgrassella alvi and Gilliamella apicola. This initial survey is the first step in understanding how the prophage community interacts with, and possibly modulates, bacterial communities in the honey bee gut.