The maternal microbiome during pregnancy and the peripartum period plays a critical role in maternal health outcomes and establishing the neonatal gut microbiome, with long-term implications for offspring health. However, a healthy microbiome during these key periods has not been definitively characterized. This longitudinal study examines maternal and neonatal microbiomes using 16S rRNA amplicon sequencing in a Japanese cohort throughout pregnancy and the postpartum period. Forty-two mothers and their forty-five offspring participate in the study. The maternal vaginal microbiome remains relatively stable during pregnancy but significantly changes in the postpartum period. Among Lactobacillus species, the Lactobacillus crispatus group is predominant. A higher abundance of Lactobacillus early in pregnancy is associated with a favorable gestational period. The maternal gut microbiome is associated with the vaginal microbiome throughout pregnancy. The neonatal gut microbiome substantially changes in early life, with bacterial composition influenced by delivery mode. Over time, bacteria shared with the maternal gut microbiome become dominant in the neonatal gut. This study provides insights into microbiome dynamics in Japanese mothers and their offspring during pregnancy and the postpartum period. Identification of common patterns across diverse populations may help define keystone microbes essential for human health and inform the development of microbiome-based interventions.