Workers of the honey bee subspecies Apis mellifera capensis (Eschscholtz) produce female offspring by thelytokous parthenogenesis and can parasitize colonies of other subspecies. In 1990, translocation of 400 colonies of A. m. capensis into the distribution area of A. m. scutellata by a commercial beekeeper triggered a dramatic parasitic phenomenon. Parasitized colonies died within a few months of infestation, and this resulted in the loss of tens of thousands of colonies by commercial beekeepers in the A. m. scutellata range in South Africa. To deal with the problem and to identify methods that would limit the impact of the social parasite, we investigated the link between beekeeping management and severity of parasitic infestations in terms of colony mortality and productivity. We demonstrate that colonies from apiaries subjected to migrations are very susceptible to infestation and consequently show dramatic mortality. Their productivity is also inferior to sedentary colonies and those in isolated apiaries in terms of honey yield and brood quantity. Furthermore, by concentrating hives in small areas and often in the vicinity of other beekeepers, cross-infestations can easily occur. This can undermine previously parasite-free beekeeping businesses. As a result of our surveys, we propose beekeeping practices based on locally trapped bees, reduced migration, and better control of parasite spread, thus promoting the conservation of these pollinators. If followed by all the South African beekeepers, these measures should limit the spread of the parasite until it is eliminated within a few years, after which full migratory beekeeping practices could resume.