Abstract:[Objective] To provide theoretical basis for using probiotics to prevent and treat the diarrhea weaning rabbit, the experiments were performed to explore the structural changes of cecum microflora in the diarrhea rex rabbit. [Methods] Total DNA were extracted from the cecum contents of 5 healthy and 5 diarrhea rex rabbits respectively. PCR-DGGE and Real-Time PCR were applied to analyze the differences of Cecum microflora between the healthy and diarrhea rex rabbits. [Results] Through the analysis we found that the richness, evenness and diversity index of PCR-DGGE profiles bands were not significant difference. But clustering analysis and Principal Component Analysis (PCA) could distinguish diarrhea group from healthy group. Real-Time PCR detection showed that in the diarrhea rabbit, despite the number of the population of normal intestinal flora including Prevotella, Clostridium clusterⅠ was not changed (P>0.05), the population of Streptococcus spp., Clostridium leptum group, Bi?dobacterium spp., Clostridium coccoides, Ruminococcus albus, Butyrivibrio fibrisolvens, Fusobacterium rausnitzii were sharply decreased (P<0.01). However, the number of Escherichia coli, which belongs to the Enterobacteriacae family, was greatly increased (P<0.05). [Conclusion] The results prove that the population of probiotics decreased, some harmful microorganism quantity increased in the cecum of diarrhea rex rabbit, the cecum flora structure is difference but not significant (P>0.05), indeed the structure of flora has a tendency to complicate in the diarrhea rabbit.