Abstract: The study aims to identify the pathogenic species of the Acoitum mosaic plant from Jiangyou, Sichuan Province, which is the local production area of Aconitum, and analyze the characteristics of the pathogenic species by polymerase chain reaction (RT-PCR) in respect of molecular. Specific primers of coat protein (cp) of cucumber mosaic virus (CMV) from Zhongba Jiangyou were designed, then cloned, transformed and sequenced. A 375 bp gene fragment was identified as CMV and named CMV- FZ. The sequence of 375 gene fragment was an effective code region of amino acid, coding 125 amino acid residues. The phylogenetic tree of different CMV isolates was established by the coat protein nucleotide sequence, and then the proteomics was analyzed for this sequence. Compared with the study result of CMV virus subgroup isolates cp gene, the sequence similarity was 74.8%-98.2% and 73.4%-99.2% for nucleotide and amino acid respectively, and the similarity to CMV virus subgroup II was 96.1%-98.2% and 96.0%-99.2% respectively. CMV- FZ embraced the highest amino sequence similarity with CMV-PCT2 from China, up to 99.2%. Genetic evolution analysis showed that the affinity of CMV-FZ, Chinese isolates (Zin and Hubei-1) and American isolates (DKRD) was the closest, they were together in the same branch of the phylogenetic tree, belonged to the CMV subgroup II. The above results exhibited that Acontium accompanied with mosaic disease was infected with CMV.