In recent years, the survival of the Western honeybee, Apis mellifera, an important pollinator, has been severely threatened by climate change, habitats loss, pesticides, pathogens and other environmental pressures. Gut microbiota plays an important role in honeybee metabolism, growth, development, disease resistance and immune response. Honeybees contain relatively simple, but highly specialized, gut microbiota, which can be cultured in vitro and used as a model for insect gut microbiota in general. Based on domestic and overseas research, we elaborated the composition of the gut microbiota of honeybees, their distribution in the gut, and how they respond to environmental change, especially when challenged by pathogens and during host growth and development. In addition, we discuss measures to protect honeybees and the key obstacles to improved protection and utilization of these essential insects.