To assess the effects of different habitat conditions on the genetic diversity of Apis cerana cerana, 2400 individual workers from 120 colonies in four localities of South Anhui mountainous area were analyzed using microsatellite DNA loci. Results showed that in the tea tree monoculture, the number of alleles, average expected heterozygosity and polymorphism information content showed no significant difference with those in the natural forest. The number of alleles and polymorphic information content in domesticated population were significantly different from those in the wild population. The average expected heterozygosity was not significantly different between those two populations. The number of alleles, the average expected heterozygous and polymorphic information content were significantly different from those in the wild for samples collected in 2006. There was significant genetic differentiation among populations, with an average differential coefficient of 0.32. Our results indicated that the cultivation of tea plantation in South Anhui would not affect the genetic structure and conservation of bees.