A consistent marker for Colony Collapse Disorder (CCD) in the honeybee has been detected and identified by Mass Spectrometry based proteomics (MSP). The analysis of honeybees from commercial apiaries across the United States and from a research observation hive discovered an iridescent virus (Iriodoviridae, IIV) that was significantly discriminated among strong, failing, and collapsed honeybee colonies. A relationship between IIV and the Microsporidia Nosema was further discovered using the same techniques. This combination of IIV and Nosema that is the consistent marker of CCD. MSP proved to be a rapid, automated analysis method that features an unrestricted capability to detect and identify multiple pathogens in a single analysis.