Our goal was to evaluate the molecular basis of metronidazole resistance in the bacterial vaginosis-associated organism Atopobium vaginae. Bacterial vaginosis (BV) affects up to 29% of women and is the leading cause of vaginal discharge. BV is associated with a shift in the vaginal microbiota from commensal Lactobacillus spp. to a diversity of fastidious anaerobic and facultative organisms, including A. vaginae. BV is treated with metronidazole but recurrent disease affects more than half of treated women within on year. One contributing factor to recurrent disease could be metronidazole resistance among BV-associated organisms such as A.vaginae. To gain a greater understanding of the molecular mechanism of metronidazole resistance in this organism we sequenced a susceptible (minimum inhibitory concentration = 16 micrograms/ml) clinical isolate for comparative studies with metronidazole-resistant isolates.