Oyster (Crassostrea gigas) extract (OE) contains many nutritional and functional components, including glycogen, taurine, and zinc. Our previous study showed that dietary OE increased the relative composition of Lactobacillus in cecal contents of rats. However, it was not clear whether this increase in Lactobacillus following the addition of dietary OE also occurs in mice. The present study demonstrated the effects of dietary OE on the composition of the microbiota and short-chain fatty acids in the feces of mice. Male C57BL/6J mice were divided into four groups and fed an AIN-93G diet (LF diet), AIN-93G modified high-fat diet (HF diet), LF diet containing 5% (w/w) OE (LFOE diet), and 5% (w/w) HF diet containing OE (HFOE diet) for 56 days. The composition of the fecal microbiota was compared between groups following high-throughput 16S rRNA gene amplicon sequencing using the Ion PGM system. The relative abundance of Lactobacillus in the feces of OE fed mice was significantly higher than in mice fed an OE free diet. These results suggest that dietary OE increased the relative composition of Lactobacillus not only in rats but also in mice.