The data produced by sequencing are unambiguous, reproducible and portable, thus offering the advantage that public databases can be constructed. In Kenya, screening for T. vaginalis is not routinely done. However, recent studies have indicated that there is high prevalence of T. vaginalis among different groups in Kenya [26–29]. Despite this, no typing has been carried out. In this study, we genotyped T. vaginalis isolated from pregnant women attending ANC in Kilifi, Kenya.