Rhinoviruses (RVs) are the most common etiological agent implicated in respiratory infections among infants and children. There are currently no approved antivirals and vaccine for use against the virus; hence, the need for information on the genotypes of rhinovirus from developing countries of the world with high burden of the infection. This study determined the genotypes of rhinovirus circulating among children in selected cities in Nigeria. Nasopharyngeal and oropharyngeal samples were carefully collected from children showing signs of respiratory infection in two communities in South-west Nigeria. Polymerase Chain Reaction was used to amplify the hypervariable part of the 5\'- non-coding region, the entire viral protein gene 4 and the 5\' terminus of the VP2 gene of RV. Nucleotide BLAST and phylogenetic analyses were used to genotype the isolates. Of the samples analysed, 12.7% showed rhinovirus positivity. All the three genotypes of rhinovirus were detected with genotype C (71.4%), being the predominant. Multiple strains of rhinovirus were found circulating. We showed for the first time the genotypes and strains of rhinovirus circulating in Nigeria. Further studies are required to highlight transmission patterns and disease severity among rhinovirus species in Nigeria.