This study examined the effects of L-arabinose on mouse intestinal microbiota and urinary isoflavonoids. Male mice were randomly divided into two groups: those fed a 0.05% daidzein-2.5% L-arabinose diet (AR group) and those fed a 0.05% daidzein control diet (CO group) for 28 days. The amounts of daidzein detected in urine were significantly lower in the AR group than in the CO group. The ratio of equol/daidzein was significantly higher in the AR group (p<0.01) than in the CO group. The composition of caecal flora differed between the AR and CO groups. The occupation ratios of Prevotella and Lactobacillales were significantly lower in the AR group. This study suggests that dietary L-arabinose has the potential to affect the metabolism of equol from daidzein by altering the metabolic activity of intestinal microbiota.