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Cervical cancer exerts a significant public health burden globally and in India. While HPV-16 and HPV-18 are well-known etiological agents, emerging evidence highlights the regional significance of other high-risk genotypes like HPV-58 and HPV-59. This study aimed to evaluate the prevalence and cytological associations of HPV genotypes, particularly 58 and 59, in Northeast Indian women. A total of 429 cervical swab specimens were collected from women attending the routine outpatient department at NEIGRIHMS, Shillong, between 2021 and 2025, following informed consent and institutional ethical approval. Cytological analysis and demographic data collection were performed. HPV genotyping was carried out at the reference lab at Pune using the Xpert HPV assay and qPCR Panel. Among 429 participants, 74 (17.25%) tested positive for HPV. Among the HPV positive cases, the genotype distribution was: HPV-16 (52.70%), HPV-18 (8.10%), and HPV-58(5.40%) and HPV-59 (13.51%). Notably, HPV-58 positive women exhibited abnormal cytology, while HPV-59 positive patients (n = 10), Pap smears showed NILM (6), ASC-US (1), Bacterial vaginosis (2), and One case of Poorly Differentiated Malignancy. This study underscores the emerging clinical relevance of HPV-58 and 59 in Northeast India. The higher cytological abnormality in HPV-58 cases highlights the need for expanded HPV genotyping in screening programs.