Background: Preterm birth presents a challenge on a global scale with a disease burden that is on the rise. It is a leading cause of perinatal morbidity and mortality worldwide with approximately 15 million preterm births every year. Kenya has a 12% preterm birth rate with about 190,000 babies born preterm every year. The female lower genital tract bacterial community plays a vital role in maternal and neonatal health. An association between altered vaginal microbial composition and preterm birth has been demonstrated in previous studies. However, findings in terms of composition and diversity of these bacteria across the few studies available have differed. With the progress and increased availability of using gene sequencing based techniques, the contribution of these vaginal microbial community changes to preterm birth have emerged as an area for research focus. Study Objective: The study objective was to compare the vaginal microbiota of women who presented with spontaneous preterm labour with those with term labour using 16S ribosomal RNA gene sequence-based techniques. Methodology: The study was a case control study set in AKUH Nairobi labour ward. Vaginal swabs were collected from mothers who presented between 26 weeks to 36 weeks of gestational age with diagnosis of preterm labour as well as controls matched for age and parity who presented in labour past 37 weeks of gestation. The vaginal microbiota of women who were in preterm labour was compared to those in term labour using 16S ribosomal RNA (rRNA) gene sequences. Results: In total, 100 participants were recruited for the study with 50 cases of preterm labour and 50 matched controls. Vaginal gene sequencing was done for 46 cases and 19 control with high quality reads achieved from 52 samples. The vaginal microbiota in both study groups was rich in the Lactobacillus genus of organisms. Fourty seven samples (90.4%) had a microbiota rich in different Lactobacillus species including unclassified Lactobacillus (n=35), Lactobacillus. iners (n=23), Lactobacillus. helviticus (n=18), Lactobacillus. vaginalis (n=17), Lactobacillu.mucosae (n=2), Lactobacillus. zeae (n=1) and Lactobacillus. coleohominis (n=1) existing with several overlaps. There was high diversity of the vaginal microbiota although it did not fall into any assigned community state type. Conclusions: This study demonstrates a spectrum of diversity in the vaginal microbiota without clear evidence of any specific microbiota patterns that have a correlation with preterm labour.