Objectives To determine the molecular epidemiology of seven coxsackievirus A16 (CVA16) strains previously reported by this research group. Methods Full-length VP1 and VP4 sequences were obtained and phylogenetic analyses were performed. Results Six strains were classified as genotype C. Moreover, one divergent strain not clustered in any of the three currently reported genotypes was found. Conclusion This is the first report of CVA16 in Peru and provides valuable baseline data about its potential distribution in South America, as well as evidence of a potential divergent genotype that has never before been reported.