The ectoparasitic mite Varroa destructor Anderson and Trueman (Acarina: Varroidae) shifted host from Eastern honeybees Apis cerana Fabricius (Hymenoptera: Apidae) to Western honeybees Apis mellifera Linnaeus (Hymenoptera: Apidae) with disastrous consequences globally. The high genetic diversity of V. destructor and abundant opportunities for cross-species transmission probably promoted this host shift. Whether Varroa underwoodi (Acarina: Varroidae) also exhibits these traits is unknown. Here, we conduct a large-scale survey across China on the occurrence, morphology, reproduction, and genetics of V. underwoodi in A. cerana and A. mellifera colonies to fill gaps in our knowledge of this mite and to determine whether host shifts occurred. Despite the large number of colonies screened, V. underwoodi was exclusively found in A. cerana, where it occurred at low infestation rates. Three genetic clades were detected in the V. underwoodi population, which differed neither in morphology nor in reproductive ability. Nevertheless, the genetic diversity of V. underwoodi is likely to increase chances for host shifts, even though opportunities for cross-species transmission seem low. More studies of the neglected Varroa species seem appropriate to enable a better understanding of host shifts in the Apis spp./Varroa spp. system and evaluate the potential risk they pose to apiculture with A. mellifera.