In this study, real–time fluorescence quantitative PCR was used to investigate the variance of 13 bacteria communities in the different section of gastrointestinal tract (GIT) in a clinical death red panda. The investigated 13 bacteria showed variance in amount in the GIT. Enterobacteriaceae accounts for the major bacteria with its logarithm of bacterial DNA copies is 9.35. The mount of Ruminococcus albus and Ruminococcus flavefaciens was higher in the rectum, with the logarithmic values of bacterial DNA copies, 5.29 and 3.91, respectively. However, other detected bacteria remained higher number in the colon, and the logarithmic values of bacterial DNA copies of Butyrivibrio fibrisolvens, Megasphaera elsdenii, and Clostridium cluster IV were 9.03, 6.06, and 9.13, respectively. Compared with the stomach, the bacteria communities were significantly different in the jejunum, colon and rectum of the red panda (P<0.05). In conclusion, the jejunum, colon and rectum may play an important role in the growth of red panda. Enterobacteriaceae is the most abundant bacteria in the GIT and is worthy of further study.