In this study, honey bees ( Apis mellifera L.) were exposed to LD 05 and LD 50 doses of five commonly used acaricides for controlling the parasitic mite, Varroa destructor . LD 50 values at 48 h post-treatment showed that tau-fluvalinate was the most toxic, followed by amitraz, coumaphos, thymol, and formic acid. However, the hazard ratios, which estimate the hive risk level based on a ratio of a standard dose of acaricide per hive to the LD 50 of the acaricide, revealed that tau-fluvalinate was the most hazardous followed by formic acid, coumaphos, amitraz, and thymol. The expression of the honey bee acetylcholinesterase gene increased after treatment with the LD 05 and LD 50 acaricide doses and could distinguish three patterns in the timing and level of increased expression between acaricides: one for amitraz, one for tau-fluvalinate and formic acid, and one for coumaphos and thymol. Conversely, changes in cytochrome P450 gene expression could also be detected in response to all five acaricides, but there were no significant differences between them. Changes in vitellogenin gene expression could only detect the effects of tau-fluvalinate, amitraz, or coumaphos treatment, which were not significantly different from each other. Among the acaricides tested, coumaphos, amitraz, and thymol appear to be the safest acaricides based on their hazard ratios, and a good marker to detect differences between the effects of sub-lethal doses of acaricides is monitoring changes in acetylcholinesterase gene expression.