Growth of microorganisms inside honey bees, and particularly by commensal organisms that compete with pathogens preventing their colonization, is an important factor in bee health, suggesting that keeping bees healthy may be more important than treating colonies. It is critical to diagnose and treat the honey bee diseases and prevent colony losses, which necessitates routine monitoring of the microflora and its components. In this chapter, standard methods for isolation, cultivation, and identification of microflora are given along with a summary and classification of commensal and pathogenic organisms and their dynamic. Especially relevant for stabilization of the microflora for proper health are the changes in microflora composition over the seasons (winter, spring, summer, and autumn) with regard to climate change, bacterial interactions for developing new approaches to disease control to avoid commercial antibiotics, and an understanding of microflora ecology as it pertains to the health of the bee colony. After determining the standard dynamic of microflora, probiotics and prebiotics can be considered.