In this study, we investigated genetic diversity of the giant panda (Ailuropoda melanoleuca) in two populations in China, one in unfragmented mountain area and the other in seriously fragmented population. Some great changes were ascertained in genetic diversity such as the reduction of total number of scored DNA bands obtained by the method of multi-locus DNA fingerprinting, the increased band sharing coefficient and the reduction in heterozygosity. These results suggest that the giant panda may be much more sensitive to habitat fragmentation than some other species.