Fucoxanthin is a xanthophyll-type carotenoid that provides many benefits to human health. However, the mechanism by which fucoxanthin interacts with microbes and inhibits pathogenic bacteria is unknown. In this study, we investigated the effects of fucoxanthin isolated from the edible seaweed Undaria pinnatifida on pathogenic bacteria Escherichia coli and lactobacilli both in vitro and in vivo. Fucoxanthin strongly inhibited the growth of Gram-positive pathogenic bacteria but was less effective against Gram-negative bacteria. Fucoxanthin extracted from the crude mixture had a recovery rate of 93.38% and a purity of 82.70%, which were higher than those of fucoxanthin extracted using a previous method. Fucoxanthin also promoted the growth of intestinal microbes in mice. Fucoxanthinol, a metabolite of fucoxanthin, was generated in the culture media. Fucoxanthin can be deacetylated into fucoxanthinol not only by conventional digestive enzymes in the digestive tract, but also by E. coli and lactobacilli in the intestine. These results indicate that fucoxanthin interacts with and influences E. coli and lactobacilli in the intestine. Therefore, fucoxanthin isolated from Undaria pinnatifida possibly can be applied in human health maintenance.