A moderate sequence heterogeneity isolate (JY-2) of CTV infecting Chinese wild mandarin (C. daoxianensis S.W. He) in were examined by RT-PCR and next-generation sequencing (NGS) of RNA sequencing (RNA-seq). Complete genomic sequences of JY-2 consisted of 19112 nucleotides (nts) were determined. Based on evidence of genomic characteristics, sequence analysis, and phylogenetic analysis of JY-2, one putative novel CTV genotypes JY should be considered. RT-PCR results showed that JY genotype was only in Chinese wild mandarin (C. daoxianensis) trees from Jiangyong (Hunan Province), China. These results will underpin further understanding of the molecular diversity of CTV and will provide a new insight into its evolution.