[Objectives]  Apis cerana is an economically essential insect that plays a significant role in pollination and that is well adapted to different ecological environments in China. Population genetic research can provide a basis for the discovery, protection and utilization of the genetic resources of this species. Guangxi province is the main A. cerana producing region in China. [Methods]  Genetic differentiation, genetic characteristics and genetic diversity of A. cerana were analyzed in Guangxi using 33 morphological markers, 38 microsatellite markers and a mitochondrial marker of a tRNA^leu-COⅡ fragment. [Results] None of a suite of analytical methods, including morphological stepwise discriminant-cluster analysis, principal component-cluster analysis, microsatellite DAPC, structure analysis, cluster analysis, F_st value, mitochondrial F_st value or AMOVA, found evidence of genetic differentiation in A. cerana in Guangxi. However, although microsatellite genetic diversity of bees from different sample sites in Guangxi was relatively similar, differences were apparent in mitochondrial markers which are susceptible to influence by human factors. Acmt01001 was the main mitochondrial haplotype at 9 sample sites with little human influence. However, the mitochondrial genetic structure at the Beiliu and Beihai sites obviously differed from that at other sites in that 2 or 3 haplotypes other than Acmt01001 were the main haplotypes, a situation probably caused by unscientific breeding and other artificial interference. [Conclusion]  The population size of A. cerana in Guangxi is large and gene flow is frequent. There is no evidence of genetic differentiation over a range of 650 km. In order to protect and utilize the locally adapted genetic resources of A. cerana we suggest that a nature reserve be established.