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The small hive beetle (SHB), Aethina tumida Murray, is a parasite of honey bee colonies and causes the fermentation of honey as well as colony collapse. Outbreaks have been confirmed in Africa, America, Europe as well as Asia, where an outbreak was reported in the Philippines and South Korea in 2014 and 2017, respectively. In South Korea, in September 2016, this honey bee parasite was first identified in apiaries in Miryang, Gyeongnam Province. However, the invasion pathway of SHB has not been identified, and honey bee pathogens harbored by SHB have not been well characterized. Therefore, phylogenetic analysis of SHB with the use of COI gene and detection of fourteen common honey bee pathogens were conducted in this study. The confirmation of the fourteen honey bee pathogens in SHB showed that this beetle carries black queen cell virus and deformed wing virus. Therefore, SHB could have a role in the spread of these viruses. The way of entry of the SHB to South Korea remains undetermined, but the phylogenetic analysis of the COI gene revealed that it was most similar to species found in the USA. There is an urgent need for national-level monitoring and quarantine measures for preventing the spread of SHB infestation in South Korea.