Human papillomavirus infection is a prevalent viral condition affecting the female reproductive system, with high-risk HPV (hrHPV) posing significant risks. The vaginal microbiome plays a crucial role in the progression of cervical intraepithelial neoplasia (CIN). This study investigates the correlation between cervicovaginal microbiota and HPV status in cervicovaginal samples collected from 173 randomly selected participants enrolled in a clinical trial assessing self-sampling for HPV typing. Employing linear discriminant analysis effect size and receiver operating characteristic methodologies, microbial diversity across different cervical lesion categories was examined, identifying potential bacterial species as markers for cervical abnormalities. Among the cases analyzed, the positive predictive value of HPV infection was 74.2%, with Fannyhessea vaginae showing a relative abundance exceeding 0.00123%. This research also investigated the relationship between HPV alpha 7 and alpha 9 and various bacterial species. The findings indicated a potential association between HPV alpha 7 and Streptococcus, particularly Streptococcus pyogenes. Further observational studies are warranted to establish the association between vaginal microbiota dysbiosis and the carcinogenic potential of (hr)HPV-induced cervical cancer. The proposed microbiological biomarkers hold promise for reducing unnecessary invasive procedures and facilitating CIN risk assessment.