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In order to identify potential threats to genetic diversity of native honeybees, the genetic diversity of the existing honeybee population in Germany was assessed for the first time. Two thousand representative samples of worker bees from selected honeybee colonies were genetically sequenced. The breeds Apis mellifera mellifera, Apis mellifera carnica and Buckfast bees were included in the assessment. Furthermore, the breeding structure was determined through surveys of beekeepers and breeders. The findings indicate a fluid transition between those who breed bees and those who simply keep them. In Germany, 750 honeybee breeders are registered in professional associations.