In recent years, large-scale losses of honeybee (Apis mellifera) colonies have taken place in Europe and North America. Apiculture scientists have organized a CoLoss Network to investigate and explain these losses. This article presents survey results and analyses of honeybee (Apis mellifera L.) colony mortality from 2009 to 2013 in 12 provinces in China, analyses of the proportions of colony mortality, and their possible causes. Standard questionnaires were used in this survey, as supplied by CoLoss, and financial support was provided by the European Cooperation in Science and Technology (COST). All statistical analyses were performed using R statistical software. A generalized linear mixed effects model (GLMM) was used to analyze potential risk factors. In total, more than 5300 beekeepers responded to the survey. This included less than half of the Apis cerana survey data set. A total of 3742 apiaries, which were part of the valuable Apis mellifera dataset that contains 520653 colonies, were also statistically analyzed in this paper. Average mortality over the winters of 2009-2013 was estimated to be 8.9%. The loss (12%) during the winter of 2011-2012 was higher than in other years. This level of mortality was considered acceptable by beekeepers and apiculture scientists. There was substantial variation in total loss by province (range 2.3%-19%). Xinjiang Province and Henan Province differed significantly from other provinces in their average loss. Average loss also differed significantly by type of operation, such as commercial, part-time, and sideline operations, although part-time and sideline operations did not differ significantly from each other during most surveyed years. Xinjiang Province and Henan Province have large numbers of commercial beekeeping operations. Province and operational data were calculated collectively, and the results supported the hypothesis that commercial beekeeping operations caused frequent honeybee queen failure and fostered the spread of other diseases, confirming that these were the two causes of colony loss. Colony collapse disorder (CCD) was not a common problem in China until recently. Overall rates of colony loss were low in general, with differences among operations of different sizes and among different provinces. The GLMM results highlighted several factors that have a significant effect on winter losses. The frequency of comb renewal and problems with the queens were responsible for most losses. The rates of colony mortality were considered acceptable, and the symptoms of colony mortality did not match those of CCD. The parasitic mite Varroa destructor was not found to be the main cause of these losses. This is because beekeepers regularly treat colonies for Varroa destructor in early spring before the queens lay most of their eggs and again in late fall. This twice-yearly treatment kept the colonies in normal or better conditions before the onset of winter. Improving the frequency of comb renewal, strengthening the prevention and control of bee mites and other diseases, monitoring the queens, and increasing the use of the new queens may keep colony mortality within acceptable ranges. This is the first nationwide investigation of Apis mellifera colony losses. These results could help prevent and control honey bee colony losses in China.