Objective To investigate the changes of the intestinal mucosa-associated microbiota in the patients with ulcerative colitis (UC), and to explore their correlation with the clinical manifestations. Methods From June to October 2016, at Gastrointestinal Endoscopy Center, the Second Affiliated Hospital of Xi′an Jiaotong University, 28 patients with UC and 16 healthy individuals who underwent colonoscopy examination were enrolled. The mucosa specimens of them were collected for fluorescent in situ hybridization (FISH). The bacterial flora were observed and counted, the correlation between the bacterial flora and the clinical manifestations were analyzed. Kruskal-Wallis test and Spearman rank correlation analysis were performed for statistical analysis. Results Among 28 patients with UC, 16 were at active phase and 12 at remission phase. The number of total bacteria flora, Escherichia coli, Clostridium and Bacteroides of the active UC group and remission UC group were all more than those of healthy control group; however the number of Lactobacillus and Bifidobacteria were less than those of healthy control group, and the differences were statistically significant (χ2=23.34, 19.94; 23.40, 12.96; 23.39, 19.16; 23.32, 10.46; 23.19, 4.25; 18.94, 12.33; all P<0.05). The number of total bacteria flora, Escherichia coli and Bacteroides of the active UC group were more than those of the remission UC group, however the number of Lactobacillus and Bifidobacteria were less than those of the remission UC group, and the differences were statistically significant (χ2=7.32, 5.63, 5.62, 20.38 and 4.82; all P<0.05). In the patients with UC, the defecation frequency was positively correlated with the count of Bacteroides (r=0.459, P=0.014) and was negatively correlated with the count of Lactobacillus (r=-0.634, P<0.01). In UC patients, bloody stool, endoscopic appearance and total Mayo score were positively correlated with the counts of universal bacteria, Escherichia coli and Bacteroides (r=0.469, 0.403, 0.376; 0.604, 0.562, 0.475; 0.551, 0.463, 0.461; all P <0.05); and which were negatively correlated with Lactobacillus and Bifidobacteria (r=-0.570, -0.413; -0.899, -0.458; -0.862, -0.480; all P<0.05). The evaluation by the doctors was positively correlated with the counts of Escherichia coli (r=0.415, P=0.028), however was negatively correlated with Lactobacillus and Bifidobacteri (r=-0.841, -0.529; both P<0.01). Conclusion The intestinal microbiota have sigificantly changed in patients with UC which are correlated with some clinical manifestations of UC. Key words: Colitis, ulcerative; In situ hybridization, fluorescence; Mucosa associated microbiota; Clinical manifestations