We have examined sequence variability among nine isolates of hop stunt viroid (HSVd) collected from hop gardens in Tohoku district in Japan, the only area in the world where hop stunt disease is endemic. Six different consensus and one-consensus sequences as well as 12 sequence variants were detected in the nine HSVd-hop isolates, which suggested the sequence of HSVd-hop was remarkably variable. A neighbor-joining analysis was carried out on the new HSVd-hop sequences together with 44 previously described variants of HSVd isolated from hop and other species. All the HSVd-hop sequences recovered from hops cultivated in the Tohoku district of Japan as well as the type isolate and two Korean isolates form a cluster with the HSVd-g subtype 1 commonly recovered from grapevine. This close relationship between HSVd-hop and -grapevine isolates strongly supports the grapevine origin for hop stunt disease.