This study aims to provide an overview of the diversity of intestinal Lactobacillus among Chinese patients with hepatitis B virus (HBV)-related decompensated cirrhosis and who received liver transplant for hepatitis B cirrhosis. Fecal samples were collected from 38 healthy volunteers, 61 patients with HBV-related decompensated cirrhosis (group LC) and 74 patients who had liver transplant for hepatitis B cirrhosis (group LT). Quantitative polymerase chain reaction technology with species-specific primers was applied to investigate lactobacilli 16S rDNA in crude DNA, extracted from fecal samples. Software package Statistical Package for the Social Sciences and Palaeontological Statistics for Windows was used to analyze the data. Lactobacilli population of the two patient groups was different from the healthy control subjects, principal differences being marked decrease in the population of Lactobacillus rhamnosus (p < 0.001 for both patient groups) and reduction in the frequency of Lactobacillus fermentus (p < 0.001 for group LC and p < 0.01 for group LT). Our findings on the frequency of lactobacilli population suggested decreased diversity in groups LC and LT (compared with the healthy controls (p < 0.001 and p < 0.01, respectively)). Patients tended to have less complex fecal lactobacilli composition than the healthy controls, especially in the group LC.