The complete genome sequence of passiflora virus Y (PaVY) from passion fruit growing in Guangdong province, China, was determined. The entire positive single-strand RNA genome comprises 9681 nucleotides (nt) excluding the poly(A) tail and encodes a polyprotein of 3084 amino acids flanked by 5' and 3' untranslated regions of 169 and 257 nt, respectively. In sequence comparisons and phylogenetic analysis, PaVY appears to represent a new species in the bean common mosaic virus subgroup of the genus Potyvirus. This is the first report of the complete genome sequence of PaVY and the first report of this virus in China.