The genome sequence of a novel species of the genus Waikavirus (the family Secoviridae), which we named Brassica napus RNA virus 1 (BnRV1), was identified in a rapeseed (Brassica napus) transcriptome dataset. The BnRV1 genome was 12,293 nucleotides long followed by a poly(A) tail. Two open reading frames (ORFs), called ORF1 and ORFX, were predicted. The larger ORF, ORF1, encodes a polyprotein of 3,471 amino acids and the smaller ORF, ORFX, overlaps ORF1 and encodes an 87 aa long protein of unknown function. The BnRV1 ORF1 polyprotein was predicted to undergo proteolytic processing to yield seven mature proteins, including an RNA-dependent RNA polymerase and three distinct coat proteins. The ORF1 and ORFX proteins share sequence similarities with the respective proteins of viruses in the genus Waikavirus, including the bellflower vein chlorosis virus, rice tungro spherical virus, and maize chlorotic dwarf virus. A phylogenetic tree inferred from a conserved segment of the polyproteins of several Secoviridae viruses confirmed that BnRV1 is a novel species of the genus Waikavirus. The BnRV1 genome sequence identified in this study may be useful for the study of waikavirus biology and waikavirus-derived diseases. Keywords: Brassica napus RNA virus 1; Waikavirus; Secoviridae; rapeseed.