Zika virus (ZIKV) transmission in the Americas was 94 first confirmed in May 2015 in Northeast Brazil1. Brazil has the highest number of reported ZIKV cases worldwide (>200,000 by 24 Dec 20162) and the most cases associated with microcephaly and other birth defects (2,366 confirmed by 31 Dec 20162). Following the initial detection of ZIKV in Brazil, >45 countries in the Americas have reported local ZIKV transmission, with 24 of these reporting ZIKV-associated severe disease3. Yet the origin and epidemic history 100 of ZIKV in Brazil and the Americas remain poorly understood, despite the value of this 101 information for interpreting observed trends in reported microcephaly. To address this we generated 54 complete or partial ZIKV genomes, mostly from Brazil, and report data generated by a mobile genomics lab that travelled across Northeast (NE) Brazil in 2016. One sequence represents the earliest confirmed ZIKV infection in Brazil. Analyses of viral genomes with ecological and epidemiological data estimate that ZIKV was present in NE Brazil by February 2014 and likely disseminated from there, nationally and internationally, before the first detection of ZIKV in the Americas. Estimated dates of the international spread of ZIKV from Brazil indicate the duration of pre-detection cryptic transmission in recipient regions. NE Brazil’s role in the establishment of ZIKV in the Americas is further supported by geographic analysis of ZIKV transmission potential and by estimates of the virus’ basic reproduction number.