To evaluate alterations in fecal bacterial compositions in weaning piglets after supplementation with Phellodendron Cortex extract (PCE), piglets were allowed freely to consume feed containing 10 ppm of PCE for 7 weeks. During the feeding period, fecal samples were collected from individual piglets. A total of 578 valid sequence reads were generated from 40 fecal samples of normal piglets before supplementation with PCE. Fifteen classes were identified. Approximately 90% of classifiable sequences belonged to Clostridia and Bacilli classes. The abundance of Clostridium spp. and Lactobacillus spp. was determined based on the results of the sequencing. The supplementation with 10 ppm PCE for 3 weeks increased the numbers of Clostridium spp. and Lactobacillus spp. whereas seven weeks of supplementation with PCE reduced their abundance. In vitro, PCE inhibited the growth of E. coli and Salmonella enteritidis in a dose-dependent manner.