The Varroa mite, Varroa destructor, a parasitic mite that afflicts honey bees, has become increasingly resistant to acaricides like fluvalinate due to its widespread use. The target site insensitivity mechanism, mediated by the L925V/M/I mutations in the voltage-gated sodium channel, plays a major role in resistance. Additionally, cytochrome P450 monooxygenases (Cyp450s) appear to function as a metabolic resistance factor; however, no Cyp450-mediated resistance mechanism has been reported to date. The aim of this study was to identify and characterize Cyp450s associated with fluvalinate resistance. A synergistic bioassay confirmed the involvement of Cyp450s in conferring tolerance or resistance to fluvalinate. Correlation analysis between mortality data and the expression levels of Cyp450 genes led to the identification of several candidates that may play a crucial role in fluvalinate resistance. Analysis of tissue distribution patterns revealed that these genes were most abundantly expressed in the cuticle and synganglion. This suggests that, despite their relatively low expression level, they may play a critical role in protecting the target site from fluvalinate due to its predominant expression in neuronal tissues. Functional analysis, in conjunction with baculovirus expression, demonstrated that fluvalinate has high inhibition rates against the recombinant candidate Cyp450s, suggestive of their strong interaction with fluvalinate. We discussed the potential utilization of their expression levels as a molecular marker for diagnosing metabolic resistance in field-collected Varroa mites.