Abstract: The genetic diversity and genetic differentiation of honeybees (Apis cerana cerana) from 6 samplings in Wuyi Mountain nature reserve were studied with five microsatellite markers. The results were as follows: total 23 alleles were detected, mean polymorphic information content (PIC) was from 0.402 9 to 0.497 8 and mean heterozygosity (He) was from 0.452 5 to 0.561 3.Through Fisher's exact text, there were significantly difference genetic structures among honeybees from the six sampling points (P0.01) and the genetic differentiation was occurred. Genetic differentiation coefficients (FST) were from 0.020 0 to 0.143 5. Especially there was significant honeybee population genetic differentiation between honeybees from Masu and others, and between the peak and the west foot of mountain, forming independence populations. The gene flow interrupted by surrounding high mountains.