Human Papilloma Virus (HPV) infection is the primary cause of virtually all cervical cancers. Cervical cancer despite being largely preventable is still the leading cause of gynaecological cancer related death among females in developing countries. This study was carried out to molecularly characterized Human Papilloma Virus among women attending selected hospitals in Sokoto, Sokoto State, Nigeria. This study involves the analysis of high vaginal swab obtained from 208 women. The high vaginal swab samples were analysed using PCR, DNA sequencing and phylogenetic analysis of the identified genotypes. Only two Human papilloma virus genotypes (HPV type 18 and 58) were detected in this study with Human papilloma virus type 58 as the most prevalent. This study identified only two Human papilloma virus genotypes (HPV types 18 and 58) in Sokoto, Nigeria which can serve as basis for establishing vaccine in the study area.