The intestinal microbiota of 10 pups (five from dam A and five from dam B) in the suckling stage (18 days old) and at maturity (40 days old) were compared with those of their dams to assess the mechanisms of bacterial transmission during development of intestinal microbiota in the rat model. Fecal samples were subjected to amplified ribosomal DNA restriction analysis and 65 operational taxonomic units (OTUs) were identified. The intestinal microbiota of mature pups were more complex than those of the suckling stage. Most of the OTUs present in dams were detected in their pups at maturity. These common OTUs accounted for more than 70% of the clones of libraries generated from both groups of pups. In contrast, the number of OTUs in pups that were not shared by their dams was larger than the number they had in common. These bacteria were presumably transmitted horizontally from environmental sources. However, these OTUs accounted for less than 30% of the clones generated from both groups of pups. This study suggested that vertically transmitted bacteria were the predominant component of the intestinal microbiota of pups, although the diversity of intestinal microbiota during pup growth was influenced by horizontal transmission.