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Purpose: Human papillomavirus detection is crucial in determining preventive approach in cervical cancer. Different HPV genotypes have been reported worldwide and have shown variations with respect to geographic location and oncogenic capabilities. We aimed to conduct molecular characterization and phylogenetic analysis of human papillomavirus (HPV) in Northern Nigeria, to guide public health intervention. Methods: Cervical smear samples were collected from 148 consenting subjects attending different Hospitals in Northern Nigeria. It was stained with Papanicolaou method and processed for molecular detection of HPV. Isolates of HPV were sequenced targeting HPVL1 gene. The sequences were analysed for single-nucleotide polymorphism. HPV variant lineages and relatedness was determined by phylogenetic analysis. Results: The result of the present study showed that 26.4% (34) of the subjects had HPV infection. The result of the cytodiagnosis showed that 29.4% (10/34) had normal cytology, 23.5% (8/34) had ASCUS, and 20.6% (7/34) had LSIL, while those having HSIL and SCC accounts for 20.6% (7/34) and 5.9% (2/34), respectively. The result for sequence analysis shows about fifteen different circulating genotypes in Northern Nigeria. Out of these, HPV 16 has the highest frequency (20.6%), while HPV 11, 70, 18, 31, 33, 35, 52, 56 and 7 has the least frequency (2.9%) each. Total of 21 single-nucleotide polymorphisms were detected, out of which 15 are synonymous, while 6 are non-synonymous mutations. Phylogenetic analysis of HPV genotypes using maximum likelihood method showed that majority of HPV genotypes from Nigeria clustered with two undetermined lineages. Pairwise distance estimation of some sequences from this study and some reference sequence revealed a distance ranging from 0.0082 to 2.0994, indicating that the sequences are majorly closely related. Conclusion: The present study provided important data about molecular epidemiology, characteristics, phylogeny and polymorphism which will aid in further studies that will advance in-depth understanding of the viral molecular epidemiology and possibly policy on public health intervention.