ABSTRACT: It is a widespread practice in China to keep colonies of both the western honey bee, Apis mellifera, and the eastern honey bee, Apis cerana, in close proximity. However, this practice increases opportunities for spillover of parasites and pathogens between the two host bee species, impacting spatial and temporal patterns in the occurrence and prevalence of the viruses that adversely affect bee health. We conducted a 1-year large-scale survey to assess the current status of viral infection in both A. mellifera and A. cerana in China. Our study focused on multiple aspects of viral infections in honey bees, including infection rate, viral load, seasonal variation, regional variation, and phylogenetic relationships of the viruses within the same species found in this study and other parts of the world. The survey showed that the black queen cell virus (BQCV), deformed wing virus (DWV), Israeli acute paralysis virus (IAPV), and sacbrood virus (SBV) were common in both A. mellifera and A. cerana, and infection dynamics of BQCV, DWV, and SBV between bee species or seasons were significantly different. DWV was the most common virus in A. mellifera, and its infection rate and load in A. mellifera were higher than those in A. cerana, which reflects the high susceptibility of A. mellifera to Varroa destructor infestation. The infection rate and viral load of SBV were higher in A. cerana than in A. mellifera, indicating that SBV poses a greater threat to A. cerana than to A. mellifera. Our results also suggested that there was no geographical variation in viral dynamics in A. mellifera and A. cerana. Phylogenetic analyses of BQCV, DWV, IAPV, and SBV suggested the cross-regional and cross-species spread of these viruses. This study provides important insights into the complex relationships between viruses and their hosts in different seasons and regions, which will be important for developing effective disease management strategies to improve bee health.