Abstract:The coat protein(CP) gene of Leek yellow stripe virus isolated from garlic in Xiamen(LYSV-XM) was sequenced in order to investigate its molecular variation and relation to the groups. It revealed that the nucleotide and deduced amino acid sequence identities were 79.2%~99.1% and 79.5%~99.3% respectively by comparison between LYSV-XM and other isolates. Phylogenetic analysis of 29 isolates based on nucleotide sequences of CP gene showed that all isolates were clustered into four groups. LYSV-XM and four isolates from China (AB194642, AB194641), New Zealand (DQ402056) and United Arab Emirates (AB0005611) shared 98.5%~99.5% similarities at nucleotide level, and formed GroupⅠ.