A molecular analysis pipeline consisting of custom microarray, polymerase chain reaction (PCR), quantitative PCR (qPCR) and ultra deep sequencing was employed to characterize the honey bee microbial flora. Pathogen screening was performed using the ''Arthropod Pathogen Microarray'' (APM) built on the same design principles used for human pathogen microarray screening [44, 45] . The array's design couples highly-conserved nucleic acid targets with hybridization-based detection to identify previously uncharacterized organisms [46, 47, 48, 49, 50, 51] . Specifically, the APM was designed to detect virtually all known microbial parasites of insects. Endpoint PCR provided sensitive detection while qPCR documented abundance of select pathogens. Ultra deep sequencing facilitated the discovery of novel and highly divergent microbes. Together the results from our monitoring study provide insight regarding the incidence of virus and microbe infections in honey bee colonies.