We determined the complete genome sequences of two isolates of cnidium vein yellowing virus (CnVYV-1 and -2) that co-infected all field samples collected from Cnidium officinale in Korea. Unlike CnVYV-2, however, CnVYV-1 was sap-transmissible to Nicotiana benthamiana. CnVYV-1 and -2 have bipartite genomes of 7,263 and 3,110 nucleotides and 7,278 and 3,112 nucleotides, respectively, excluding the poly(A) tails. Phylogenetic analysis of the CnVYV-1 and -2 sequences indicated close relationships to strawberry latent ringspot virus, an unassigned member of the family Secoviridae. CnVYV-1 and CnVYV-2 are closely related viruses that may represent a tentative new species of the family Secoviridae.