Background: Much controversies have been associated with the pathogenicity of Mycoplasma hominis but little has been done to unravel the mystery  behind the different views. This study aimed at investigating the genetic variants abounding within M. hominis and the distribution of the virulent genes among the variants. Methodology: Twenty (20) M. hominis isolates from high vaginal swabs of women (11 from pregnant women and 9 from women presenting with  infertility) attending the Obstetrics and Gynaecology clinics of Nnamdi Azikiwe University Teaching Hospital (NAUTH), Nnewi, Nigeria, were sequenced  using 16S rRNA universal gene target for the purpose of phylogenetic analysis and epidemiological typing. The isolates were also screened for the  presence of M. hominis variable adherence antigen (vaa) and p120 virulent genes using primer constructs from the respective genes in a conventional  PCR protocol. Results: Of the 20 M. hominis vaginal isolates, 4 phylogenetic strains were detected; strain MHS43 constituted 10/20 (50.0%) [2/9 (22.2%) from infertile  women and 8/11 (72.7%) from pregnant women]; strain MHBS constituted 3/20 (15%) [3/9 (33.3%) from infertile women and 0/11 (0%) from pregnant  women]; strain MHSWP2 constituted 4/20 (20.0%) [3/9 (33.3%) from infertile women and 1/11 (9.1%) from pregnant women]; while strain MHKC87  constituted 3/20 (15%) [1/9 (11.1%) from infertile women and 2/11 (18.2%) from pregnant women]. Each of vaa and p120 genes was detected in 14 of 20  isolates, while 6 isolates did not carry the genes. A 2-way ANOVA test showed that none of the genes was significantly associated with a particular strain  (p=0.8641). Conclusions: The different views regarding the pathogenicity of M. hominis may be linked to the heterogeneity within the species and lack of  omogeneity in the virulent genes as witnessed both in the intra species and intra strain levels.