Objective To analyze the sequence of Hantavirus(HV) from Zhejiang, Fujian provinces and Shanghai municipal. Methods The sequence of M segment of several HV strains from coastal areas of Zhejiang, Fujian province and Shanghai municipal were collected and analyzed by Mega 4.0 and DNAStar software, phylogenetic trees were built by neighbor joining method (NJ) and analyzed to compare the similarity of HV strains isolated from Zhejiang, Fujian provinces and Shanghai municipal. Results The phylogenetic tree revealed that the similarity of isolates in the same province is much higher than the other, meanwhile, in same province or city, the nucleotide similarity of the same region is higher than the other regions. The distributions of the isolates from closer regions share higher sequence similarity in the phylogenetic branches. The ZH53 strain of HTN isolated from Fujian province, Gou3 strain and ZJ5 strain of SEO isolated from Jiande region in Zhejiang province formed a distinct phylogenic lineage in HTNV clade and SEOV clade respectively, and these strains were different from other variants and international standard strains with the similarity of 82.7%-86.3% and 84.0%-85.3% respectively. The SEOV strains in Zhejiang were isolated from field mouse indicating the phenomenon of “host spillover”. Conclusion The sequence similarity and the phylogeny of HV in southeast costal area of Zhejiang, Fujian provinces and Shanghai is closed related to the isolated regions, indicating geographic distribution of HV.