Background: The role of the gut microbiome in the onset and development of atopic dermatitis (AD) has been postulated. Therefore, we investigated the gut microbial compositions in infants with and without AD, and compared it to the gut bacterial flora of their mothers. Methods: This was a prospective and cross-sectional study. Among 44 pairs of mothers and children, we selected infants who were born via full-term normal vaginal delivery and that had no history of antibiotic or probiotic use, and infection during the first three months of life. The 15 pairs, consisting of nine healthy infants and six AD infants, were included in this study. Fecal samples of mothers and infants were analyzed within 30 days of delivery and at 12 months of age. Microbes in the fecal samples of mothers and infants were subjected to analysis of 16S rRNA amplicon sequencing. Results: Abundance of specific taxonomic groups was notably different, but microbial diversity and phylogenetic distances were not significantly different in either maternal or infant groups according to the presence of infant AD. A total of 12 species were selected as differential species in infants with AD compared to healthy infants. Six species were significantly different in the mothers of infants with AD compared to the mothers of healthy infants. Akkermansia muciniphila was only detected in healthy infants and their mothers. Conclusions: These data indicated that the presence of Akkermansia muciniphila in mothers and children after vaginal delivery is associated with the onset and development of AD.