34 captive Giant Pandas (captive population: including a population and b population) and 7 captive wild Giant Pandas (captive wild population) are study objects. Their blood samples are got from Chengdu Research Base of Giant Panda Breeding and China Research and Conservation Center for the Giant Panda. 30 microsatellite DNA markers including AY161177～AY161218, Ame-μ5～Ame-μ70 and g001～g905 are used to investigate the actual state of genetic diversity within and between samples. Meanwhile, the measures how to maintenance and improve genetic diversity of Giant Pandas are discussed. The information for microsatellite locus showed that 30 microsatellite DNA markers were polymorphic (PIC=0.621～0.640) and the genetic diversity of 41 captive Giant Pandas was higher (a population: A=5.48, Ho=0.475, He=0.690; b population: A=5.24, Ho=0.453, He=0.719; captive wild population: A=3.80, Ho=0.514, He=0.725) than that of other 6 endangered species(Ho=0.210～0.390, He=0.150～0.430), but was lower than that of 3 non-endangered species. 41 captive Giant Pandas maintenanced high genetic diversity. However, compared to 7 captive wild Giant Pandas, the genetic diversity of 34 captive Giant Pandas degraded. The date of F-statistics and gene flow (of 25 microsatellite locus Nm=2.610, Fst=0.0874, Fit= 0.4116) indicated that a population and b population exchanged individuals resulting to inbreeding. There was a low level of genetic variabilities between a population and b population. The inbreeding level of b population was higher than that of a population (a population: Fis=0.3221，b population: Fis=0.3983). Therefore, at the present, the focus of management of captive Giant Panda should shift to avoiding the inbreeding and the loss of genetic diversity. The captive populations of Giant Panda should be in the same management unit. Retrieving pedigree and chosing the fittest exchange individual are the key point. Microsatellite technologey is the key way to protect and improve genetic diversity of captive Giant Pandas.