Our study was limited by the small number of isolates, which rendered it difficult to investigate the implication of TVV carriage on clinical signs and symptoms. Despite the low number of T. vaginalis isolates, the presence of all four types of TVVs in our isolates, in addition to the five actin genotypes, demonstrates there is notable genetic diversity of T. vaginalis isolated from pregnant women in Kilifi, Kenya. Isolates of the most prevalent actin genotype E lacked TVVs; further studies with higher number of strains should be conducted in order to corroborate these results. The actin gene should be considered as a potential genetic marker for molecular epidemiology and genotypic traits of T. vaginalis.