Technical Abstract: Infectious diseases are a component of the environment in which the organism exists and such an environment must be critically controlled in the dense population structures of a social organism. Honey bee pathogens can be devastating to the colony. Two of the most important are the bacterium Paenibacillus larvae and the fungus Ascosphaera apis. Here we report draft genome sequences for these two pathogens, as a prelude to more extensive genome annotation and functional analyses. The draft sequences of P. larvae and A. apis were produced by whole genome shotgun approach and have been deposited in GenBank. P.larvae genome assembly produced contigs that spanned over 4 Mb, that represents about 10x coverage of the genome. The predicted genes were compared to sequences in GenBank with BLAST and the resulting automated annotation is available at www.hgsc.bcm.tmc.edu/microbe/plarvae. The draft sequence of A. apis was assembled into contigs that totaled 21.6 Mb in length. This represents about 7x genome coverage. The contigs were joined into the scaffolds that are suitable for gene predictions (in progress). With the completion of the sequence of honey bee genome, interest in it’s pathogens is intensified. Knowledge of the genetic makeup of two of the major pathogens of honey bees now offer a broad view of host-pathogen interactions at the systems biology level and an opportunity to elucidate the infectious processes of these microbes including virulence factors and accessory elements needed for infection.