The study was aimed to analyze the intestinal microflora of Elaphe taeniura by using the polymerase chain reaction–denaturing gradient gel electrophoresis (PCR–DGGE) and fluorescent quantitative–polymerase chain reaction (Q–PCR) techniques. The results shown that diversity index of bacteria in jejunum, ileum and rectum of E. taeniura were 2.84, 3.14, and 2.69, respectively; and evenness was 0.78, 0.86, and 0.74; richness was 17.20, 23.40, and 14.80, respectively. Sequence analysis results revealed that the microfloras were mostly Firmicutes and Bacteroidetes. Q–PCR results showed that the abundance of total bacteria, firmicutes and bacteroidetes were more than 108.07, 106.82 and 106.30 CFU/g respectively; the abundance of Clostridium, Lactobacillus and Akkermansia all reached to 105.05 CFU/g, and they had the trend of increase at first and decrease later, and the abundance of rectum was lower than that of jejunum; the abundances of Enterococcus and Entero bacteriaceae were more than 106.11 CFU/g, the abundance of rectum was higher than that of jejunum. The results suggested that the dominant intestinal flora in E. taeniura were Bacteroidetes and Firmicutes; and their abundance both increased at first and then decreased wherever in jejunum, ileum and rectum; the abundance of probiotics in rectum were lower than in jejunum; while, harmful bacteria in rectum were higher than that in jejunum.