Distribution of honey bee pathogens detected in colonies before, during, and after almond pollination. Honey bee samples were obtained from monitor colonies from October 2013 to June 2014. PCR was used to test for 16 honey bee-infecting pathogens including: viruses (ABPV, BQCV, CBPV, DWV, IAPV, KBV, SBV, LSV1, LSV2, LSV3, LSV4, and LSV5, microsporidia (N. ceranae), bacteria (P. larvae and M. plutonius), and trypanosomatids (C.m./L.p.). Pathogen occurrence, the frequency of detecting a specific pathogen as a percentage of the total number of positive tests, was assessed at different time periods throughout the study. There were 155 positive tests in bee samples collected before almond pollination (October–December 2013), 79 positive tests during almond pollination (February), 223 positive tests immediately after almond pollination (March–May), and 130 positive tests from 20 colonies that were sampled in June 2014.