Abstract Red-osier dogwood (ROD) extract contains a lot of polyphenols that have the potential for modulation of gut microbiota. However, little information is available about its prebiotic properties. This study investigated the impact of ROD polyphenol extract on the ileal microbiota with dietary supplementation of ROD polyphenol extract in a pig model. The data indicated that supplementation of ROD polyphenol extract significantly increased class Bacilli, order Lactobacillales and family lactobacillaceae. Within family lactobacillaceae, Lactobacillus was the main responder by increasing from 5.92% to 35.09%. Further analysis showed that ROD polyphenol extract improved two species Lactobacillus delbrueckii and Lactobacillus mucus. The results of this study suggested that ROD polyphenol extract has the potential to play prebiotic role and confer health benefit through modifying gut microbiota.