Picea asperata Mast., which occurs in a restricted habitat in western China, has a wide ecological amplitude. In the present study, ten natural populations of P. asperata were studied using AFLP markers to investigate the population genetic structure and the level of genetic diversity. Of the 210 loci identified with two EcoRI/MseI primer combinations, 142 loci were found to be polymorphic. Yet, the level of genetic diversity observed within populations was quite low. The averages of NEI’s gene diversities (h) and Shannon's indices of diversity (I) calculated across populations equaled 0.156 and 0.227, respectively. The coefficient of gene differentiation among populations, based on the estimate GST and the unbiased estimate Φst, equaled 0.340 and 0.231, respectively. The mean genetic distance (D) between population pairs was 0.119 (range 0.050-0.156). Such high values indicate that there is significant differentiation among populations of P. asperata. Several factors could have contributed to the strong population differentiation, including relatively limited gene flow between populations (Nm = 0.968). Variation in environmental conditions and consequent selection pressures may be other factors attributing to the high level of genetic differentiation among populations. In addition, it was discovered that the geographic distances are not correlated with the genetic distances between the populations of P. asperata.