Between the years of 2015 and 2016, Brazil was surprised by an exanthematous disease outbreak with symptoms distinct from dengue. During the same period, an increase of microcephaly and Guillain-Barré syndrome cases were observed in the northeastern region of the country. Investigation led to the discovery that it was the Zika virus (ZIKV) infection, and its relationship with neurological complications was later established. Phylogenetic studies with ZIKV have been done in Brazil. Here, we sequenced the ZIKV E gene from strains that occurred in the states of Paraná and Mato Grosso do Sul, Brazil, in 2016. To do this, two pair of primers were developed aiming to sequence the entire ZIKV E gene (1500bp). Due to the low Viral Load of the ZIKV in the peripheral blood, a Semi-Nested PCR was standardized, aiming to increase the sensitivity of the technique. Samples were sequenced by ACT Gene Análises Moleculares Ltda. (Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil). Maximum Likelihood and Maximum Credibility trees were built using the SEAVIEW and Mr. Bayes 3.2 software, respectively, and the phylogenetic signal was determined. Of 33 samples provided by Laboratório Central do Estado do Paraná (LACEN-PR), only 8 were able to be sequenced: 4 from Mato Grosso do Sul and 4 from Paraná. The ZIKV E gene sequences obtained in this study started in the position 904 following until position 2343, providing a 1440 bp fragment of the 1500 that make up the gene. An overlap region of 48 bp was observed. The Maximum Likelihood and Maximum Credibility trees showed similar structure: two major genotypes – African and Asian – were found, being the African genotype divided in two main lineages. All new sequences obtained in this study were clustered in Brazilian branches, within the Asian genotype. The quartets analysis based on the ZIKV E gene showed a low phylogenetic signal, with more than 40% of quartets unresolved, which means that the ZIKV E gene is highly similar across different strains of the virus, mainly in American strains. Therefore, these results demonstrated that, based on the E gene sequences, ZIKV seems to be converging into a new lineage within Asian genotype.