Intestinal microbiota plays an important role in nutrition, metabolism and immunity in all mammals. It is comprised of diverse populations of bacteria and other microorganisms whose abundances are impacted by both environmental and host genetic factors. However, the understandings of the intestinal microbiota in different pig breeds remain largely undefined. To examine the differences in intestinal microflora between two pig breeds with different genetic backgrounds under the same environment, 16S rRNA gene amplification and sequencing were performed to investigate the structural composition and potential functions of microbial communities in rectum and caecum of Erhualian and Sushan pigs. The results revealed that the diversity of intestinal microflora in two pig breeds was similar, but the abundance of specific intestinal microflora was different. At the phylum level, the dominant bacteria in caecum and rectum of Erhualian and Sushan pigs were Firmicutes, Acidobacteria and Bacteroides, but their expression abundance was different. Firmicutes and Bacteroidetes in Erhualian pigs were higher than those in Sushan pigs. At the genus level, Lactobacillus was the most abundant in caecum of Sushan pigs (6.83%) and rectum of Erhualian pigs (9.61%), while Ruminococcaceae UCG-005 were dominant in caecum of Erhualian pigs (10.89%) and Streptococcus in rectum of Sushan pigs (24.89%). This study further confirmed the existence of specific microbial community diversity and abundance in different pig breeds. The microbial community diversity and abundance in Erhualian and Sushan pigs were closely related to pig fat deposition and nutrient absorption.