To our knowledge, this is the first study determining T. vaginalis genotypes and co-occurrence of T. vaginalis viruses in Kenya. We sequenced the actin gene for 22 isolates and identified five types of T. vaginalis by in silico RFLP-analysis of the amplified actin gene. We found notable genetic diversity by full actin gene sequence analysis among T. vaginalis isolates in Kilifi, as well as those retrieved from GenBank. Prevalence of T. vaginalis in this study (6.6% in 349 pregnant women) was high but, however, fell short of the prevalence of T. vaginalis among women aged 15–49 years in the World Health Organization Africa region in 2012, which was estimated to be 11.5% (95% CI: 9.0–14.6) . This is suggestive of lower rates of T. vaginalis among the general population of women in Kilifi, Kenya compared to other African countries .