A survey for Prunus necrotic ringspot virus (PNRSV) in an orchard of Prunus cerasus cv. Montmorency and Prunus avium cv. Hedelfingen in New York by enzyme-linked immunosorbent assay indicated an eightfold higher infection rate in sour cherry (33%, 32 of 96) than in sweet cherry (4%, 6 of 136) trees. The presence of PNRSV was confirmed by reverse transcription-polymerase chain reaction and amplification of the coat protein (CP) gene in total RNA from infected leaf tissue. Latent infection was prevalent in the majority of trees infected (87%, 33 of 38), while a few of them exhibited shock symptoms or had severely reduced growth (13%, 5 of 38). Asymptomatic PNRSV-infected trees clustered in spatial proximity to symptomatic trees. Sequence analysis of the CP gene (675 bp) indicated a population structure consisting of one predominant molecular variant for 10 isolates and six minor molecular variants for seven isolates. A high sequence identity was found between the CP gene of PNRSV isolates from cherry trees and other isolates from diverse hosts and various geographic origins at the nucleotide and amino acid levels (88 to 100%). Phylogenetic analyses showed a clustering of PNRSV isolates from cherry trees in New York in the predominant group PV-96.