Background The vaginal microbiota (VMB) plays a key role in women’s reproductive health. VMB composition varies with ethnicity, making it necessary to characterize the VMB of the target population before interventions to maintain and/or improve the vaginal health are undertaken. Information on the VMB of Thai women is currently unavailable. We therefore characterized the VMB in normal Thai women. Methods Vaginal samples derived from 25 Thai women were subjected to 16S rRNA gene next-generation sequencing (NGS) on the Ion Torrent PGM platform. Results Two groups of VMB were detected, lactobacilli-dominated (LD) and non-lactobacilli dominated (NLD) groups. Lactobacillus iners was the most common species found in the LD group while Gardnerella vaginalis followed by Atopobium vaginae and Pseudumonas stutzeri were commonly found in the NLD group. Conclusions The VMB patterns present in normal Thai women is essential information to further determine the factors associated with VMB patterns in vaginal health and disease and to develop proper management of reproductive health of Thai women.