The importance of honey bees to global agriculture and the emergence of CCD calls for increased longitudinal monitoring of infectious processes within honey bee colonies. The data presented herein represent the finest resolution time-course of honey bee associated microbes to date. We demonstrate the utility of an arthropod pathogen microarray (APM) for simultaneous detection of numerous pathogens and the power of ultra deep sequencing for viral discovery. Several previous studies examined honey bee samples from diseased or CCD-affected and healthy colonies [9, 10, 20, 75, 76] , but few have temporally monitored multiple pathogens [60, 77, 78] . Although these studies differed in sampling strategy, geography, colony management (e.g. migratory commercial versus stationary hobbyist, chemically treated versus organic), and pathogen monitoring technology (e.g. serology, PCR, spore counts, microarray) they provide a framework for our surveillance of previously characterized honey bee pathogens.