The gut microbiota of children is linked to the development of disorders later in life. Recent discoveries that demonstrated the presence of the meconium, amniotic fluid, and placenta microbiota have called into question the sterile womb paradigm. The PacBio single-molecule real-time circular consensus sequencing technique was used in the study to investigate the maternal origin of the microbiota of neonatal meconium. High-fidelity reads of full-length 16S rRNA genes may be generated with this method, increasing the sensitivity and specificity of taxonomic profiling. It also decreased the possibility of false positives. The microbiota of 39 maternal-neonate couples was studied using full-length 16S rRNA-based maternal samples (amniotic fluid, feces, vaginal fluid, saliva) and first-pass meconium. Microbiota traits specific to sample types were discovered using alpha- and beta-diversity analysis. The amniotic fluid and vaginal fluid microbiotas were dominated by sequences from different genera; the meconium microbiota was dominated by Bacillus and Escherichia/Shigella; the maternal fecal microbiota was dominated by Bacteroides and Faecalibacterium, and the maternal saliva microbiota was dominated by Streptococcus and Prevotella. Furthermore, in all sample types, distinct operational taxonomic units (OTUs) were found. The meconium microbiota and the microbiota of numerous mother samples had similar OTUs, according to dyad analysis. The maternal fecal and vaginal microbiota had more traits with the amniotic fluid microbiome than the meconium microbiota. The findings strongly recommend that the meconium microbiota was seeded from various maternal body locations, with the amniotic fluid microbiota contributing the most to meconium microbiota seeding among the maternal body sites studied.