The Chinese black honey bee is a distinct honey bee subspecies distributed in the Xinjiang, Heilongjiang and Jilin Provinces of China. We conducted a study to investigate the genetic origin and the parasite/pathogen profile on Chinese black honeybees. The phylogenetic analysis indicated that Chinese black honeybees were two distinct groups: one group of bees formed a distinct clade that was most similar to Apis mellifera mellifera and the other group was a hybrid of the subspecies, Apis mellifera carnica, Apis mellifera anatolica and Apis mellifera caucasica. This suggests that the beekeeping practices might have promoted gene flow between different subspecies. Screening for pathogens and parasites showed that Varroa destructor and viruses were detected at low prevalence in Chinese black honeybees, compared with Italian bees. Further, a population of pure breeding black honeybees, A. m. mellifera, displayed a high degree of resistance to Varroa. No Varroa mites or Deformed wing virus could be detected in any examined bee colonies. This finding suggests that a population of pure breeding Chinese black honeybees possess some natural resistance to Varroa and indicated the need or importance for the conservation of the black honeybees in China.