Background: Genetic evidence of asymptomatic Mycoplasma hominis (M. hominis) and Ureaplasma urealyticum (U. urealyticum) infection associated with infertility among females is lacking because suitable high throughput molecular methods have not been applied. Objective: This study aimed to explore the occurrence of M. hominis and U. urealyticum in the genital tract of females with asymptomatic infection and infertility as well as determine their genetic relatedness. Materials and Methods: The study group included 100 asymptomatic females and 31 females diagnosed with infertility. Sequencing of the 16S rRNA gene following DNA extraction was performed directly from endo-cervical swabs. Phylogenetic analysis established the genetic linkage between the isolates from both groups. Results: In asymptomatic females, M. hominis and U. urealyticum were detected with a prevalence of 8% and 2% respectively. Among females with infertility, the prevalence was 6.45% and 3.23% for M. hominis and U. urealyticum respectively. In both groups, M. hominis occurred significantly more frequently. Phylogenetic analysis revealed three distinct clusters in both groups: two with already characterized M. hominis and Ureaplasma species (28.6% of the overall Mycoplasma spp.) and one distinct cluster matched with U. urealyticum. Furthermore, all M. hominis from asymptomatic females clustered significantly with infertility contrary to U. urealyticum. The M. hominis cluster was significantly linked to two strains from China. Conclusion: The sequence analysis of Mycoplasma and Ureaplasma in the genital tract of asymptomatic and infertile females showed significant association; therefore, it is paramount to consider them as possible etiologic agents of infertility and genital infection, especially when the etiology of infertility is unknown. Key words: Mycoplasma hominis, Ureaplasma urealyticum, Genetic linkage, Asymptomatic infections, Infertility.