The Modern beekeeping industry is being challenged by the varroan mite and its transmitted pathogens.

Various types of Varroa destructor exhibit different levels of virulence toward honey bees, but only the

Japanese (J) and Russian (R) types were found to infect Apis mellifera. Type R was more highly virulent

against A. mellifera in comparison with type J. Examining the genetic profile of Varroa species is therefore

of crucial importance in apiary management. In this study, maternally inherited mitochondrial cytochrome

oxidase I (COI) and bisexual nuclear internal transcribed spacer (ITS) sequences of V. destructor

individuals from Taiwan were determined. All 168 COI sequences observed in populations obtained

from A. mellifera were identical and belonged to type J, with one base difference to that of populations

collected from A. cerana; the new type is named ‘T type’ (Taiwan type). ITS sequences of V. destructor

and its sister species V. jacobsoni were identical. A network analysis based on 611 COI sequences

compiled from references indicated the presence of 27 haplotypes in V. destructor. Epidemic history and

relationship analyses of V. destructor showed that the basal haplotypes were those from A. cerana and

many R-extending haplotypes infesting A. mellifera involving amino acid substitutions. Calibration dating

based on COI analysis revealed that V. destructor differentiated from its sibling lineage (occurring in Sri

Lanka) prior to 1.3 million years ago (Mya). The ancestral haplotype retention and drift in V. destructor

that occurred locally during 0.10–0.64 Mya might be relevant to its host A. cerana, which had been

isolated geologically. The highly virulent type R was spreading quickly and could gradually outcompete the

common and less virulent type J. Type T, being intermediate between types R and J, ought to be studied

to better understand the pathogenic mechanism of V. destructor in A. mellifera. Moreover, for areas where

type R does not occur, such as Taiwan, quarantine requirements are crucial for reducing invasion risks.