Background:Zika virus (ZIKV) has emerged as a global pathogen causing significant public health concs.China has reported several imported cases where ZIKV were carried by travelers who frequently travel between China and ZIKV-endemic regions.To fully characterize the ZIKV strains isolated from the cases reported in China and assess the risk of ZIKV transmission in China,comprehensive phylogenetic and genetic analyses were performed both on all ZIKV sequences of China and on a group of scientifically selected ZIKV sequences reported in some of the top interested destinations for Chinese travelers.Methods:ZIKV genomic sequences were retrieved from the National Center for Biotechnology Information database through stratified sampling.Recombination event detection,maximum likelihood (ML) phylogenetic analysis,molecular clock analysis,selection pressure analysis,and amino acid substitution analysis were used to reconstruct the epidemiology and molecular transmission of ZIKV.Results:The present study investigated 18 ZIKV sequences from China and 70 sequences from 16 selected countries.Recombination events rarely happens in all ZIKV Asian lineage.ZIKV genomes were generally undergone episodic positive selection (17 sites),and only one site was under pervasive positive selection.All ZIKV imported into China were Asian lineage and were assigned into two clusters:Venezuela-origin (cluster A) and Samoa-origin cluster (cluster B) with common ancestor from French Polynesia.The time of most recent common ancestors of Cluster A dated to approximately 2013/11 (95％ highest posterior density [HPD] 2013/06,2014/ 03) and cluster B dated to 2014/08 (95％ HPD 2014/02,2015/01).Cluster B is more variable than Cluster A in comparison with other clusters,but no varied site of biological significance was revealed.ZIKV strains in Southeast Asia countries are independent from strains in America epidemics.Conclusions:The genetic evolution of ZIKV is conservative.There are two independent introductions of ZIKV into China and China is in danger of autochthonous transmission of ZIKV because of high-risk surrounding areas.Southeast Asia areas have high risk of originating the next large-scale epidemic ZIKV strains.