The gut microbiota changes greatly at the onset of disease, and the importance of intestinal bacteria has been highlighted. The gut microbiota also changes greatly with aging. Aging causes skin dryness, but it is not known how changes in the gut microbiota with aging affects the expression of genes that are important for maintaining skin function. In this study, we investigated how age‐related changes in gut microbiota affect the expression of genes that regulate skin function. The gut microbiotas from young mice and aged mice were transplanted into germ‐free mice (fecal microbiota transplantation [FMT]). These recipient mice were designated FMT‐young mice and FMT‐old mice respectively, and the expression levels of genes important for maintaining skin function were analyzed. The dermal water content was significantly lower in old mice than that in young mice, indicating dry skin. The gut microbiota significantly differed between old mice and young mice. The water channel aquaporin‐3 (Aqp3) expression level in the skin of FMT‐old mice was significantly higher than that in FMT‐young mice. In addition, among the genes that play an important role in maintaining skin function, the expression levels of those encoding ceramide‐degrading enzyme, ceramide synthase, hyaluronic acid‐degrading enzyme, and Type I collagen were also significantly higher in FMT‐old mice than in FMT‐young mice. It was revealed that the gut microbiota, which changes with age, regulates the expression levels of genes related to skin function, including AQP3.