Abstract: The infected leaves of wild lily were taken from Jingyu county, Baishan city, Jilin Province.Lily mottle virus（LMoV） was detected by small RNA deep sequencing and the whole genome of LMoV Baishan-Jingyu isolate（LMOV-JY） was determined and analyzed by segmentation cloning method, in order to provide reference for detection, prevention and control of lily virus disease in Jilin Province.The results showed that the genome of LMoV-JY consisted of 9 648 nucleotides（nt）（Genbank Accession No.MT795719）.A large open reading frame（ORF） located at nt positions from 154 to 9 444 which encoding a polypeptide of 351.46 kD.By compairing with other isolates of LMoV,the nucleotide identity was from 82.82% to 97.85%,and the amino acid identity was from 92.96% to 98.64%,and it shared the highest identity with the Dalian isolate LMoV-DL（HM222521）.Amino acid sequences comparison of the CP gene of LMoV-JY with other 54 isolates in GenBank showed that all of the isolates could be divided into two subgroups.