The honey bee tracheal mite, Acarapis woodi (Acari: Tarsonemidae), is an endoparasite of honey bees. The mites feed on bee hemolymph in the tracheas of adult bees. Mite infestations cause serious damage to bee colonies. The distribution of these mites is now worldwide, from Europe to South and North America. The first recorded A. woodi infestation in the Japanese native honey bee, Apis cerana japonica, occurred in 2010. In a previous study, to determine the distribution of A. woodi in Japan, we sampled more than 350 colonies of A. cerana japonica. We found mite infestation from central to eastern Japan. On the other hand, Apis mellifera in Japan has not suffered serious mite damage. Here, to determine the effects of mite infestation on Japanese native honey bees, we investigated seasonal prevalence, mite load in the tracheal tube, and the relationship between mite prevalence and K-wing (disjointed wings). Similar to European honey bees, Japanese honey bees had a high prevalence of mite infestation in winter and a low prevalence in summer. The average mite load was about 21 or 22 mites (all stages) per trachea when all bees were infested by tracheal mites (100% mite prevalence). This mite load did not differ from that in A. mellifera. The K-wing rate was positively correlated with mite prevalence. Further comparative investigations focusing on the mechanisms of infestation will be needed to elucidate the differences in mite susceptibility between Japanese and European honey bees.