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This study reports honey bee, Apis mellifera L., colony losses that occurred in South Africa over two consecutive years. The total losses were 29.6% (95% CI: 22.8–37.5) in 2009–2010 and 46.2% (95% CI: 37.3–55.0) in 2010–2011. Furthermore, the study shows that the capensss worker social parasite, a problem unique to southern Africa, is the main perceived cause, and could explain the significant differences in the number of losses between beekeepers using the subspecies A. m. scutellata and those using the subspecies A. m. capensis. In contrast to previous studies in North America and Europe, we find a significant negative effect of migratory beekeeping practices on the extent of colony losses. Migratory beekeepers lost on average more colonies (35.5% (95% CI 29.7–47.2)) than did stationary beekeepers (17.2% (95% CI 11.2–22.3)). This was especially pronounced when the beekeepers were migrating for …