The objective of this study was to analyze the difference in intestinal microbial diversity between healthy and (Entamoeba histolytica) orally infected minipig. Enterobacterial repetitive intergenic consensus (ERIC)-PCR was applied to analyze this diversity and dynamic change, including the duodenum, jejunum, ileum, cecum, and rectum from healthy and orally infected minipig at different time points. The results showed that the intestinal microbial community of the control minipigs was stable and the ERIC-PCR band numbers of the control minipigs were the lowest in the rectum and highest in the cecum. ERIC-PCR bands of orally inoculated minipigs showed no obvious change until 24 h after postinoculation (hpi). The numbers of the ERIC-PCR bands gradually decreased from 24 to 72 hpi, then, with the development of disease, the band numbers gradually increased until 6 days postinoculation. The prominent bacteria had changed in the presence of E. histolytica infection and the DNAstar of staple of ERIC-PCR showed that obligate aerobes and facultative aerobes (Escherichia coli, Shigella, Salmonella) became the preponderant bacilli in the intestine of orally infected minipigs with E. histolytica. This study has provided significant data to clarify the intestinal microbial diversity and dynamic change of healthy and E. histolytica orally infected minipigs.