Dengue virus (DENV) is an arbovirus belonging to the genus Flavivirus, family Flaviviridae In Brazil, the reemergence and spread of DENV type 4 (DENV-4) across the country were responsible for a significant outbreak in Guaruja, Sao Paulo, Brazil. Here, we report the first genomic sequences of DENV strains circulating in Guaruja during the 2013 outbreak.